From a171b59af7203fdc5a19e6b4b8308fa1ab757e6f Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 24 Oct 2022 22:43:21 +0000
Subject: [PATCH 01/32] Update dev

---
 CHANGELOG.md    | 2 ++
 nextflow.config | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ee8bd744..e31be347 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,8 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Dev
+
 ## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-20 Maroon Tin Dalmatian
 
 ### Enhancements & fixes
diff --git a/nextflow.config b/nextflow.config
index 759cf40d..d9a384df 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -222,7 +222,7 @@ manifest {
     description     = 'Small RNA-Seq Best Practice Analysis Pipeline.'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version = '2.1.0'
+    version = '2.1.1dev'
     doi             = ''
 }
 

From 021dcb2135165272ca86dcfe31956a5cd1eb7888 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Thu, 27 Oct 2022 09:37:31 +0000
Subject: [PATCH 02/32] Fix for issue #201

---
 CHANGELOG.md                         |  2 ++
 conf/modules.config                  |  1 -
 modules.json                         |  4 ++--
 modules/nf-core/fastp/main.nf        |  5 ++++
 modules/nf-core/fastp/meta.yml       |  4 ++++
 modules/nf-core/fastqc/main.nf       | 34 ++++++++--------------------
 subworkflows/nf-core/fastqc_fastp.nf |  2 ++
 workflows/smrnaseq.nf                |  2 ++
 8 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e31be347..79e4e5cc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Dev
 
+* Updated FASTP module to allow direct addition of adapter_fasta file to it
+
 ## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-20 Maroon Tin Dalmatian
 
 ### Enhancements & fixes
diff --git a/conf/modules.config b/conf/modules.config
index 951a4719..64d851f6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -105,7 +105,6 @@ if (!params.skip_fastp) {
             params.fastp_min_length > 0    ? "-l ${params.fastp_min_length}" : "",
             params.fastp_max_length > 0    ? "--max_len1 ${params.fastp_max_length}" : "",
             params.three_prime_adapter == null ?  '' : "--adapter_sequence ${params.three_prime_adapter}",
-            params.fastp_known_mirna_adapters == null ? '' : "--adapter_fasta ${params.fastp_known_mirna_adapters}"
         ].join(" ").trim()
             publishDir = [
                 [
diff --git a/modules.json b/modules.json
index 173e2bf0..10f2aa99 100644
--- a/modules.json
+++ b/modules.json
@@ -15,11 +15,11 @@
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "1e49f31e93c56a3832833eef90a02d3cde5a3f7e"
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "f6a11408536fbee6cbea1f5977605011873de3ca"
                     },
                     "multiqc": {
                         "branch": "master",
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
index 11ea4db3..207258ad 100644
--- a/modules/nf-core/fastp/main.nf
+++ b/modules/nf-core/fastp/main.nf
@@ -9,6 +9,7 @@ process FASTP {
 
     input:
     tuple val(meta), path(reads)
+    path  adapter_fasta
     val   save_trimmed_fail
     val   save_merged
 
@@ -27,6 +28,7 @@ process FASTP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def adapter_list = adapter_fasta ? "--adapter_fasta ${adapter_fasta}" : ""
     def fail_fastq = save_trimmed_fail && meta.single_end ? "--failed_out ${prefix}.fail.fastq.gz" : save_trimmed_fail && !meta.single_end ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
     // Added soft-links to original fastqs for consistent naming in MultiQC
     // Use single ended for interleaved. Add --interleaved_in in config.
@@ -40,6 +42,7 @@ process FASTP {
             --thread $task.cpus \\
             --json ${prefix}.fastp.json \\
             --html ${prefix}.fastp.html \\
+            $adapter_list \\
             $fail_fastq \\
             $args \\
             2> ${prefix}.fastp.log \\
@@ -61,6 +64,7 @@ process FASTP {
             --thread $task.cpus \\
             --json ${prefix}.fastp.json \\
             --html ${prefix}.fastp.html \\
+            $adapter_list \\
             $fail_fastq \\
             $args \\
             2> ${prefix}.fastp.log
@@ -82,6 +86,7 @@ process FASTP {
             --out2 ${prefix}_2.fastp.fastq.gz \\
             --json ${prefix}.fastp.json \\
             --html ${prefix}.fastp.html \\
+            $adapter_list \\
             $fail_fastq \\
             $merge_fastq \\
             --thread $task.cpus \\
diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml
index 2368fded..6f6fad74 100644
--- a/modules/nf-core/fastp/meta.yml
+++ b/modules/nf-core/fastp/meta.yml
@@ -23,6 +23,10 @@ input:
         List of input FastQ files of size 1 and 2 for single-end and paired-end data,
         respectively. If you wish to run interleaved paired-end data,  supply as single-end data
         but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module.
+  - adapter_fasta:
+      type: file
+      description: File in FASTA format containing possible adapters to remove.
+      pattern: "*.{fasta,fna,fas,fa}"
   - save_trimmed_fail:
       type: boolean
       description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 05730368..55c50c87 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -8,7 +8,7 @@ process FASTQC {
         'quay.io/biocontainers/fastqc:0.11.9--0' }"
 
     input:
-    tuple val(meta), path(reads)
+    tuple val(meta), path(reads, stageAs: "?/*")
 
     output:
     tuple val(meta), path("*.html"), emit: html
@@ -20,30 +20,16 @@ process FASTQC {
 
     script:
     def args = task.ext.args ?: ''
-    // Add soft-links to original FastQs for consistent naming in pipeline
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if (meta.single_end) {
-        """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
-        fastqc $args --threads $task.cpus ${prefix}.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        END_VERSIONS
-        """
-    } else {
-        """
-        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
-        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
-        fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        END_VERSIONS
-        """
-    }
+    """
+    printf "%s\\n" $reads | while read f; do ln -s \$f ${prefix}_\$(basename \$f) ; done
+    fastqc $args --threads $task.cpus ${prefix}_*
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/subworkflows/nf-core/fastqc_fastp.nf b/subworkflows/nf-core/fastqc_fastp.nf
index b93672bf..5cec3149 100644
--- a/subworkflows/nf-core/fastqc_fastp.nf
+++ b/subworkflows/nf-core/fastqc_fastp.nf
@@ -28,6 +28,7 @@ String getFastpAdapterSequence(json_file){
 workflow FASTQC_FASTP {
     take:
     reads             // channel: [ val(meta), [ reads ] ]
+    adapter_list      // String [path/to/adapters.fa]
     save_trimmed_fail //   value: boolean
     save_merged       //   value: boolean
 
@@ -58,6 +59,7 @@ workflow FASTQC_FASTP {
     if (!params.skip_fastp) {
         FASTP (
             reads,
+            adapter_list,
             save_trimmed_fail,
             save_merged
         )
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
index 09f2c2a6..92338f25 100644
--- a/workflows/smrnaseq.nf
+++ b/workflows/smrnaseq.nf
@@ -38,6 +38,7 @@ ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config
 ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
 ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
 ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+ch_fastp_adapters          = Channel.fromPath(params.fastp_known_mirna_adapters, checkIfExists: true)
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -126,6 +127,7 @@ workflow SMRNASEQ {
 
     FASTQC_FASTP (
         ch_cat_fastq,
+        ch_fastp_adapters,
         false,
         false
     )

From 1a2a2a0c9b945c41c51bb1f9638d0949a1076e99 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 2 Dec 2022 13:57:18 +0000
Subject: [PATCH 03/32] Fix for 206 hopefully

---
 CHANGELOG.md                       | 2 ++
 modules/local/parse_fasta_mirna.nf | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e31be347..952eb2b0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Dev
 
+* [[#206](https://github.com/nf-core/smrnaseq/issues/206)] - Use % as separator in sed commands to enable conda working properly on OSX and Linux
+
 ## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-20 Maroon Tin Dalmatian
 
 ### Enhancements & fixes
diff --git a/modules/local/parse_fasta_mirna.nf b/modules/local/parse_fasta_mirna.nf
index 619cb427..4eedde8c 100644
--- a/modules/local/parse_fasta_mirna.nf
+++ b/modules/local/parse_fasta_mirna.nf
@@ -27,10 +27,10 @@ process PARSE_FASTA_MIRNA {
     fi
     # Remove spaces from miRBase FASTA files
     # sed -i 's, ,_,g' \$FASTA
-    sed '/^[^>]/s/[^AUGCaugc]/N/g' \$FASTA > \${FASTA}_parsed.fa
+    sed '%^[^>]%s%[^AUGCaugc]%N%g' \$FASTA > \${FASTA}_parsed.fa
     # TODO perl -ane 's/[ybkmrsw]/N/ig;print;' \${FASTA}_parsed_tmp.fa > \${FASTA}_parsed.fa
 
-    sed -i 's/\s.*//' \${FASTA}_parsed.fa
+    sed -i 's%\s.*%%' \${FASTA}_parsed.fa
     seqkit grep -r --pattern \".*${filter_species}-.*\" \${FASTA}_parsed.fa > \${FASTA}_sps.fa
     seqkit seq --rna2dna \${FASTA}_sps.fa > \${FASTA}_igenome.fa
 

From ae02a7607d9aba540e21ec61baaddcba4565623e Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 2 Dec 2022 14:05:23 +0000
Subject: [PATCH 04/32] FIXES 208

---
 CHANGELOG.md                              |  3 ++
 subworkflows/nf-core/fastqc_trimgalore.nf | 48 -----------------------
 workflows/smrnaseq.nf                     | 12 +++++-
 3 files changed, 13 insertions(+), 50 deletions(-)
 delete mode 100644 subworkflows/nf-core/fastqc_trimgalore.nf

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e31be347..2fb77be4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Dev
 
+- [[#208](https://github.com/nf-core/smrnaseq/issues/208)] - Fixed usability of `--skip_qc` parameter
+
+
 ## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-20 Maroon Tin Dalmatian
 
 ### Enhancements & fixes
diff --git a/subworkflows/nf-core/fastqc_trimgalore.nf b/subworkflows/nf-core/fastqc_trimgalore.nf
deleted file mode 100644
index 3eaee69f..00000000
--- a/subworkflows/nf-core/fastqc_trimgalore.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-//
-// Read QC, UMI extraction and trimming
-//
-
-include { FASTQC           } from '../../modules/nf-core/fastqc/main'
-include { TRIMGALORE       } from '../../modules/local/trimgalore'
-
-workflow FASTQC_TRIMGALORE {
-    take:
-    reads         // channel: [ val(meta), [ reads ] ]
-    skip_fastqc   // boolean: true/false
-    skip_trimming // boolean: true/false
-
-    main:
-    ch_versions = Channel.empty()
-    fastqc_html = Channel.empty()
-    fastqc_zip  = Channel.empty()
-    if (!skip_fastqc) {
-        FASTQC ( reads ).html.set { fastqc_html }
-        fastqc_zip  = FASTQC.out.zip
-        ch_versions = ch_versions.mix(FASTQC.out.versions.first())
-    }
-
-    trim_reads = reads
-    trim_html  = Channel.empty()
-    trim_zip   = Channel.empty()
-    trim_log   = Channel.empty()
-    trimgalore_versions = Channel.empty()
-    if (!skip_trimming) {
-        TRIMGALORE ( reads ).reads.set { trim_reads }
-        trim_html   = TRIMGALORE.out.html
-        trim_zip    = TRIMGALORE.out.zip
-        trim_log    = TRIMGALORE.out.log
-        ch_versions = ch_versions.mix(TRIMGALORE.out.versions.first())
-    }
-
-    emit:
-    reads = trim_reads     // channel: [ val(meta), [ reads ] ]
-
-    fastqc_html            // channel: [ val(meta), [ html ] ]
-    fastqc_zip             // channel: [ val(meta), [ zip ] ]
-
-    trim_html              // channel: [ val(meta), [ html ] ]
-    trim_zip               // channel: [ val(meta), [ zip ] ]
-    trim_log               // channel: [ val(meta), [ txt ] ]
-
-    versions = ch_versions // channel: [ versions.yml ]
-}
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
index 09f2c2a6..2f44638c 100644
--- a/workflows/smrnaseq.nf
+++ b/workflows/smrnaseq.nf
@@ -124,16 +124,16 @@ workflow SMRNASEQ {
     // SUBWORKFLOW: Read QC and trim adapters
     //
 
+    if(!params.skip_qc){
     FASTQC_FASTP (
         ch_cat_fastq,
         false,
         false
     )
-
     ch_versions = ch_versions.mix(FASTQC_FASTP.out.versions)
-
     reads_for_mirna = FASTQC_FASTP.out.reads
 
+
     //
     // SUBWORKFLOW: mirtrace QC
     //
@@ -144,6 +144,14 @@ workflow SMRNASEQ {
 
     ch_versions = ch_versions.mix(MIRTRACE.out.versions.ifEmpty(null))
 
+    } else{
+        //TODO - rob? :-)
+        
+    }
+
+
+
+
     //
     // SUBWORKFLOW: remove contaminants from reads
     //

From fff2161225693aeb6650ac04fa1c5b75ebf9bc2a Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 2 Dec 2022 14:09:59 +0000
Subject: [PATCH 05/32] Should do the trick now

---
 modules/local/parse_fasta_mirna.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/parse_fasta_mirna.nf b/modules/local/parse_fasta_mirna.nf
index 4eedde8c..e09242eb 100644
--- a/modules/local/parse_fasta_mirna.nf
+++ b/modules/local/parse_fasta_mirna.nf
@@ -27,10 +27,10 @@ process PARSE_FASTA_MIRNA {
     fi
     # Remove spaces from miRBase FASTA files
     # sed -i 's, ,_,g' \$FASTA
-    sed '%^[^>]%s%[^AUGCaugc]%N%g' \$FASTA > \${FASTA}_parsed.fa
+    sed '#^[^>]#s#[^AUGCaugc]#N#g' \$FASTA > \${FASTA}_parsed.fa
     # TODO perl -ane 's/[ybkmrsw]/N/ig;print;' \${FASTA}_parsed_tmp.fa > \${FASTA}_parsed.fa
 
-    sed -i 's%\s.*%%' \${FASTA}_parsed.fa
+    sed -i 's#\s.*##' \${FASTA}_parsed.fa
     seqkit grep -r --pattern \".*${filter_species}-.*\" \${FASTA}_parsed.fa > \${FASTA}_sps.fa
     seqkit seq --rna2dna \${FASTA}_sps.fa > \${FASTA}_igenome.fa
 

From 8eac40a27785d5220352c12686fedf51c8911e6d Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 2 Dec 2022 14:10:33 +0000
Subject: [PATCH 06/32] Fix changelog prettier

---
 CHANGELOG.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2fb77be4..3929f0c0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [[#208](https://github.com/nf-core/smrnaseq/issues/208)] - Fixed usability of `--skip_qc` parameter
 
-
 ## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-20 Maroon Tin Dalmatian
 
 ### Enhancements & fixes

From cf39b469b8874e02a82d015389141b0be0d15e2d Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 2 Dec 2022 14:11:38 +0000
Subject: [PATCH 07/32] Prettier goddamnit!

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 952eb2b0..5615588f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,7 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Dev
 
-* [[#206](https://github.com/nf-core/smrnaseq/issues/206)] - Use % as separator in sed commands to enable conda working properly on OSX and Linux
+- [[#206](https://github.com/nf-core/smrnaseq/issues/206)] - Use % as separator in sed commands to enable conda working properly on OSX and Linux
 
 ## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-20 Maroon Tin Dalmatian
 

From 55eb719eaf6de62116c012371fb022bb8c7714fb Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 2 Dec 2022 14:28:49 +0000
Subject: [PATCH 08/32] Yabadabadoooh

---
 CHANGELOG.md                                           |  2 ++
 .../execution_trace_2022-12-02_14-28-46.txt            |  1 +
 workflows/smrnaseq.nf                                  | 10 ++++++----
 3 files changed, 9 insertions(+), 4 deletions(-)
 create mode 100644 muchasmuchasgracias/pipeline_info/execution_trace_2022-12-02_14-28-46.txt

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e31be347..8ce2e696 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Dev
 
+- [[#205](https://github.com/nf-core/smrnaseq/issues/205)] - Fix mirTrace Report to be a single report again instead of per sample reports
+
 ## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-20 Maroon Tin Dalmatian
 
 ### Enhancements & fixes
diff --git a/muchasmuchasgracias/pipeline_info/execution_trace_2022-12-02_14-28-46.txt b/muchasmuchasgracias/pipeline_info/execution_trace_2022-12-02_14-28-46.txt
new file mode 100644
index 00000000..6b739acd
--- /dev/null
+++ b/muchasmuchasgracias/pipeline_info/execution_trace_2022-12-02_14-28-46.txt
@@ -0,0 +1 @@
+task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
index 09f2c2a6..77783a36 100644
--- a/workflows/smrnaseq.nf
+++ b/workflows/smrnaseq.nf
@@ -137,10 +137,12 @@ workflow SMRNASEQ {
     //
     // SUBWORKFLOW: mirtrace QC
     //
-    FASTQC_FASTP.out.adapterseq
-    | join( ch_cat_fastq )
-    | map { meta, adapterseq, fastq -> [meta + [adapter:adapterseq], fastq] }
-    | MIRTRACE
+    ch_outputs_for_mirtrace = FASTQC_FASTP.out.adapterseq
+    .join( ch_cat_fastq )
+    .map { meta, adapterseq, fastq -> [meta + [adapter:adapterseq], fastq] }
+    .collect()
+
+    MIRTRACE(ch_outputs_for_mirtrace)
 
     ch_versions = ch_versions.mix(MIRTRACE.out.versions.ifEmpty(null))
 

From 4cee6d069537c1c17cdfa97df9c0112a0dab4ba7 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Fri, 2 Dec 2022 16:32:23 +0100
Subject: [PATCH 09/32] Delete execution_trace_2022-12-02_14-28-46.txt

---
 .../pipeline_info/execution_trace_2022-12-02_14-28-46.txt        | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 muchasmuchasgracias/pipeline_info/execution_trace_2022-12-02_14-28-46.txt

diff --git a/muchasmuchasgracias/pipeline_info/execution_trace_2022-12-02_14-28-46.txt b/muchasmuchasgracias/pipeline_info/execution_trace_2022-12-02_14-28-46.txt
deleted file mode 100644
index 6b739acd..00000000
--- a/muchasmuchasgracias/pipeline_info/execution_trace_2022-12-02_14-28-46.txt
+++ /dev/null
@@ -1 +0,0 @@
-task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar

From 2e0fc78b05a6ee786d835826a7c6d6408132c7df Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 8 Dec 2022 13:14:47 +0000
Subject: [PATCH 10/32] Template update for nf-core/tools version 2.7.1

---
 .devcontainer/devcontainer.json       | 27 +++++++++++++
 .gitattributes                        |  1 +
 .github/CONTRIBUTING.md               | 16 ++++++++
 .github/ISSUE_TEMPLATE/bug_report.yml |  2 +-
 .github/workflows/ci.yml              |  8 +++-
 .github/workflows/fix-linting.yml     |  6 +--
 .github/workflows/linting.yml         | 18 +++++----
 .github/workflows/linting_comment.yml |  2 +-
 .prettierignore                       |  2 +
 CHANGELOG.md                          |  2 +-
 CITATION.cff                          | 56 ---------------------------
 README.md                             |  4 +-
 assets/slackreport.json               | 34 ++++++++++++++++
 docs/usage.md                         | 24 +++++++-----
 lib/NfcoreSchema.groovy               |  1 -
 lib/NfcoreTemplate.groovy             | 41 +++++++++++++++-----
 lib/WorkflowMain.groovy               | 18 ++++++---
 modules.json                          |  9 +++--
 modules/local/samplesheet_check.nf    |  4 ++
 nextflow.config                       | 14 +++++--
 nextflow_schema.json                  |  8 +++-
 workflows/smrnaseq.nf                 | 11 +++---
 22 files changed, 195 insertions(+), 113 deletions(-)
 create mode 100644 .devcontainer/devcontainer.json
 delete mode 100644 CITATION.cff
 create mode 100644 assets/slackreport.json

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 00000000..ea27a584
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,27 @@
+{
+    "name": "nfcore",
+    "image": "nfcore/gitpod:latest",
+    "remoteUser": "gitpod",
+
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/opt/conda/bin/python",
+                "python.linting.enabled": true,
+                "python.linting.pylintEnabled": true,
+                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
+                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
+                "python.linting.flake8Path": "/opt/conda/bin/flake8",
+                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
+                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
+                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+            },
+
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
+}
diff --git a/.gitattributes b/.gitattributes
index 050bb120..7a2dabc2 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,3 +1,4 @@
 *.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 4f0eaee3..b24dd094 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -101,3 +101,19 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
+
+## GitHub Codespaces
+
+This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+
+To get started:
+
+- Open the repo in [Codespaces](https://github.com/nf-core/smrnaseq/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
+- [Dockerfile](.devcontainer/Dockerfile)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index af04ee73..b280b79e 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -42,7 +42,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 21.10.3)_
+        * Nextflow version _(eg. 22.10.1)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 00c9d511..d0902c8c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -11,6 +11,10 @@ on:
 env:
   NXF_ANSI_LOG: false
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  cancel-in-progress: true
+
 jobs:
   test:
     name: Run pipeline with test data
@@ -20,11 +24,11 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "21.10.3"
+          - "22.10.1"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 8f76fa7f..4fe16754 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "::set-output name=result::pass"
+            echo "name=result::pass" >> $GITHUB_OUTPUT
           else
-            echo "::set-output name=result::fail"
+            echo "name=result::fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 8a5ce69b..858d622e 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -4,6 +4,8 @@ name: nf-core linting
 # that the code meets the nf-core guidelines.
 on:
   push:
+    branches:
+      - dev
   pull_request:
   release:
     types: [published]
@@ -12,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -25,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -38,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -69,12 +71,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: "3.7"
           architecture: "x64"
@@ -97,7 +99,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 04758f61..39635186 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+        run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2
diff --git a/.prettierignore b/.prettierignore
index eb74a574..437d763d 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,5 +1,6 @@
 email_template.html
 adaptivecard.json
+slackreport.json
 .nextflow*
 work/
 data/
@@ -8,3 +9,4 @@ results/
 testing/
 testing*
 *.pyc
+bin/
diff --git a/CHANGELOG.md b/CHANGELOG.md
index c54766b2..946bdd84 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.1.0dev - [date]
+## v2.1.1dev - [date]
 
 Initial release of nf-core/smrnaseq, created with the [nf-core](https://nf-co.re/) template.
 
diff --git a/CITATION.cff b/CITATION.cff
deleted file mode 100644
index 017666c0..00000000
--- a/CITATION.cff
+++ /dev/null
@@ -1,56 +0,0 @@
-cff-version: 1.2.0
-message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
-authors:
-  - family-names: Ewels
-    given-names: Philip
-  - family-names: Peltzer
-    given-names: Alexander
-  - family-names: Fillinger
-    given-names: Sven
-  - family-names: Patel
-    given-names: Harshil
-  - family-names: Alneberg
-    given-names: Johannes
-  - family-names: Wilm
-    given-names: Andreas
-  - family-names: Garcia
-    given-names: Maxime Ulysse
-  - family-names: Di Tommaso
-    given-names: Paolo
-  - family-names: Nahnsen
-    given-names: Sven
-title: "The nf-core framework for community-curated bioinformatics pipelines."
-version: 2.4.1
-doi: 10.1038/s41587-020-0439-x
-date-released: 2022-05-16
-url: https://github.com/nf-core/tools
-prefered-citation:
-  type: article
-  authors:
-    - family-names: Ewels
-      given-names: Philip
-    - family-names: Peltzer
-      given-names: Alexander
-    - family-names: Fillinger
-      given-names: Sven
-    - family-names: Patel
-      given-names: Harshil
-    - family-names: Alneberg
-      given-names: Johannes
-    - family-names: Wilm
-      given-names: Andreas
-    - family-names: Garcia
-      given-names: Maxime Ulysse
-    - family-names: Di Tommaso
-      given-names: Paolo
-    - family-names: Nahnsen
-      given-names: Sven
-  doi: 10.1038/s41587-020-0439-x
-  journal: nature biotechnology
-  start: 276
-  end: 278
-  title: "The nf-core framework for community-curated bioinformatics pipelines."
-  issue: 3
-  volume: 38
-  year: 2020
-  url: https://dx.doi.org/10.1038/s41587-020-0439-x
diff --git a/README.md b/README.md
index 9caac333..3431bbf0 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
 
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/smrnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -31,7 +31,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Quick Start
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
 
diff --git a/assets/slackreport.json b/assets/slackreport.json
new file mode 100644
index 00000000..043d02f2
--- /dev/null
+++ b/assets/slackreport.json
@@ -0,0 +1,34 @@
+{
+    "attachments": [
+        {
+            "fallback": "Plain-text summary of the attachment.",
+            "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
+            "author_name": "sanger-tol/readmapping v${version} - ${runName}",
+            "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
+            "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
+            "fields": [
+                {
+                    "title": "Command used to launch the workflow",
+                    "value": "```${commandLine}```",
+                    "short": false
+                }
+                <%
+                    if (!success) { %>
+                    ,
+                    {
+                        "title": "Full error message",
+                        "value": "```${errorReport}```",
+                        "short": false
+                    },
+                    {
+                        "title": "Pipeline configuration",
+                        "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>",
+                        "short": false
+                    }
+                    <% }
+                %>
+            ],
+            "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})"
+        }
+    ]
+}
diff --git a/docs/usage.md b/docs/usage.md
index 3d01eda4..1b923e23 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -83,9 +83,9 @@ nextflow pull nf-core/smrnaseq
 
 It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
-First, go to the [nf-core/smrnaseq releases page](https://github.com/nf-core/smrnaseq/releases) and find the latest version number - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`.
+First, go to the [nf-core/smrnaseq releases page](https://github.com/nf-core/smrnaseq/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
 
-This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
+This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
 
 ## Core Nextflow arguments
 
@@ -95,7 +95,7 @@ This version number will be logged in reports when you run the pipeline, so that
 
 Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
 
-Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. When using Biocontainers, most of these software packaging methods pull Docker containers from quay.io e.g [FastQC](https://quay.io/repository/biocontainers/fastqc) except for Singularity which directly downloads Singularity images via https hosted by the [Galaxy project](https://depot.galaxyproject.org/singularity/) and Conda which downloads and installs software locally from [Bioconda](https://bioconda.github.io/).
+Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below.
 
 > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 
@@ -104,8 +104,11 @@ The pipeline also dynamically loads configurations from [https://github.com/nf-c
 Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
 They are loaded in sequence, so later profiles can overwrite earlier profiles.
 
-If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended.
+If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment.
 
+- `test`
+  - A profile with a complete configuration for automated testing
+  - Includes links to test data so needs no other parameters
 - `docker`
   - A generic configuration profile to be used with [Docker](https://docker.com/)
 - `singularity`
@@ -118,9 +121,6 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
-- `test`
-  - A profile with a complete configuration for automated testing
-  - Includes links to test data so needs no other parameters
 
 ### `-resume`
 
@@ -169,8 +169,14 @@ Work dir:
 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
 ```
 
+#### For beginners
+
+A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters `--max_cpus`, `--max_memory`, and `--max_time`. Based on the error above, you have to increase the amount of memory. Therefore you can go to the [parameter documentation of rnaseq](https://nf-co.re/rnaseq/3.9/parameters) and scroll down to the `show hidden parameter` button to get the default value for `--max_memory`. In this case 128GB, you than can try to run your pipeline again with `--max_memory 200GB -resume` to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below.
+
+#### Advanced option on process level
+
 To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN).
-We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/software/star/align/main.nf`.
+We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/star/align/main.nf`.
 If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9).
 The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements.
 The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB.
@@ -189,7 +195,7 @@ process {
 >
 > If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly.
 
-### Updating containers
+### Updating containers (advanced users)
 
 The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`.
 
diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
index b3d092f8..33cd4f6e 100755
--- a/lib/NfcoreSchema.groovy
+++ b/lib/NfcoreSchema.groovy
@@ -46,7 +46,6 @@ class NfcoreSchema {
             'quiet',
             'syslog',
             'v',
-            'version',
 
             // Options for `nextflow run` command
             'ansi',
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
index 27feb009..25a0a74a 100755
--- a/lib/NfcoreTemplate.groovy
+++ b/lib/NfcoreTemplate.groovy
@@ -32,6 +32,25 @@ class NfcoreTemplate {
         }
     }
 
+    //
+    // Generate version string
+    //
+    public static String version(workflow) {
+        String version_string = ""
+
+        if (workflow.manifest.version) {
+            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+            version_string += "${prefix_v}${workflow.manifest.version}"
+        }
+
+        if (workflow.commitId) {
+            def git_shortsha = workflow.commitId.substring(0, 7)
+            version_string += "-g${git_shortsha}"
+        }
+
+        return version_string
+    }
+
     //
     // Construct and send completion email
     //
@@ -61,7 +80,7 @@ class NfcoreTemplate {
         misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
         def email_fields = [:]
-        email_fields['version']      = workflow.manifest.version
+        email_fields['version']      = NfcoreTemplate.version(workflow)
         email_fields['runName']      = workflow.runName
         email_fields['success']      = workflow.success
         email_fields['dateComplete'] = workflow.complete
@@ -146,10 +165,10 @@ class NfcoreTemplate {
     }
 
     //
-    // Construct and send adaptive card
-    // https://adaptivecards.io
+    // Construct and send a notification to a web server as JSON
+    // e.g. Microsoft Teams and Slack
     //
-    public static void adaptivecard(workflow, params, summary_params, projectDir, log) {
+    public static void IM_notification(workflow, params, summary_params, projectDir, log) {
         def hook_url = params.hook_url
 
         def summary = [:]
@@ -170,7 +189,7 @@ class NfcoreTemplate {
         misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
 
         def msg_fields = [:]
-        msg_fields['version']      = workflow.manifest.version
+        msg_fields['version']      = NfcoreTemplate.version(workflow)
         msg_fields['runName']      = workflow.runName
         msg_fields['success']      = workflow.success
         msg_fields['dateComplete'] = workflow.complete
@@ -178,13 +197,16 @@ class NfcoreTemplate {
         msg_fields['exitStatus']   = workflow.exitStatus
         msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
         msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
-        msg_fields['commandLine']  = workflow.commandLine
+        msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
         msg_fields['projectDir']   = workflow.projectDir
         msg_fields['summary']      = summary << misc_fields
 
         // Render the JSON template
         def engine       = new groovy.text.GStringTemplateEngine()
-        def hf = new File("$projectDir/assets/adaptivecard.json")
+        // Different JSON depending on the service provider
+        // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
+        def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
+        def hf            = new File("$projectDir/assets/${json_path}")
         def json_template = engine.createTemplate(hf).make(msg_fields)
         def json_message  = json_template.toString()
 
@@ -209,7 +231,7 @@ class NfcoreTemplate {
             if (workflow.stats.ignoredCount == 0) {
                 log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
             } else {
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
             }
         } else {
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
@@ -297,6 +319,7 @@ class NfcoreTemplate {
     //
     public static String logo(workflow, monochrome_logs) {
         Map colors = logColours(monochrome_logs)
+        String workflow_version = NfcoreTemplate.version(workflow)
         String.format(
             """\n
             ${dashedLine(monochrome_logs)}
@@ -305,7 +328,7 @@ class NfcoreTemplate {
             ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
             ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
                                                     ${colors.green}`._,._,\'${colors.reset}
-            ${colors.purple}  ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
+            ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
             ${dashedLine(monochrome_logs)}
             """.stripIndent()
         )
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 417fde67..6cbc7987 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -19,7 +19,7 @@ class WorkflowMain {
     }
 
     //
-    // Print help to screen if required
+    // Generate help string
     //
     public static String help(workflow, params, log) {
         def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
@@ -32,7 +32,7 @@ class WorkflowMain {
     }
 
     //
-    // Print parameter summary log to screen
+    // Generate parameter summary log string
     //
     public static String paramsSummaryLog(workflow, params, log) {
         def summary_log = ''
@@ -53,15 +53,21 @@ class WorkflowMain {
             System.exit(0)
         }
 
-        // Validate workflow parameters via the JSON schema
-        if (params.validate_params) {
-            NfcoreSchema.validateParameters(workflow, params, log)
+        // Print workflow version and exit on --version
+        if (params.version) {
+            String workflow_version = NfcoreTemplate.version(workflow)
+            log.info "${workflow.manifest.name} ${workflow_version}"
+            System.exit(0)
         }
 
         // Print parameter summary log to screen
-
         log.info paramsSummaryLog(workflow, params, log)
 
+        // Validate workflow parameters via the JSON schema
+        if (params.validate_params) {
+            NfcoreSchema.validateParameters(workflow, params, log)
+        }
+
         // Check that a -profile or Nextflow config has been provided to run the pipeline
         NfcoreTemplate.checkConfigProvided(workflow, log)
 
diff --git a/modules.json b/modules.json
index 70345a21..574bc334 100644
--- a/modules.json
+++ b/modules.json
@@ -7,15 +7,18 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     }
                 }
             }
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index 79054ff8..d9a84b5e 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -1,5 +1,6 @@
 process SAMPLESHEET_CHECK {
     tag "$samplesheet"
+    label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -13,6 +14,9 @@ process SAMPLESHEET_CHECK {
     path '*.csv'       , emit: csv
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script: // This script is bundled with the pipeline, in nf-core/smrnaseq/bin/
     """
     check_samplesheet.py \\
diff --git a/nextflow.config b/nextflow.config
index c9ccb710..07b9d56f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -35,6 +35,7 @@ params {
     monochrome_logs            = false
     hook_url                   = null
     help                       = false
+    version                    = false
     validate_params            = true
     show_hidden_params         = false
     schema_ignore_params       = 'genomes'
@@ -81,6 +82,7 @@ profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
         params.enable_conda    = true
+        conda.enabled          = true
         docker.enabled         = false
         singularity.enabled    = false
         podman.enabled         = false
@@ -89,6 +91,7 @@ profiles {
     }
     mamba {
         params.enable_conda    = true
+        conda.enabled          = true
         conda.useMamba         = true
         docker.enabled         = false
         singularity.enabled    = false
@@ -104,6 +107,9 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
     }
+    arm {
+        docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
+    }
     singularity {
         singularity.enabled    = true
         singularity.autoMounts = true
@@ -185,12 +191,12 @@ dag {
 
 manifest {
     name            = 'nf-core/smrnaseq'
-    author          = 'P. Ewels, C. Wang, R. Hammarén, L. Pantano'
+    author          = """P. Ewels, C. Wang, R. Hammarén, L. Pantano"""
     homePage        = 'https://github.com/nf-core/smrnaseq'
-    description     = 'Small RNA-Seq Best Practice Analysis Pipeline.'
+    description     = """Small RNA-Seq Best Practice Analysis Pipeline."""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=21.10.3'
-    version         = '2.1.0dev'
+    nextflowVersion = '!>=22.10.1'
+    version         = '2.1.1dev'
     doi             = ''
 }
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 8aaa69c5..4b6dbf49 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -176,6 +176,12 @@
                     "fa_icon": "fas fa-question-circle",
                     "hidden": true
                 },
+                "version": {
+                    "type": "boolean",
+                    "description": "Display version and exit.",
+                    "fa_icon": "fas fa-question-circle",
+                    "hidden": true
+                },
                 "publish_dir_mode": {
                     "type": "string",
                     "default": "copy",
@@ -217,7 +223,7 @@
                     "type": "string",
                     "description": "Incoming hook URL for messaging service",
                     "fa_icon": "fas fa-people-group",
-                    "help_text": "Incoming hook URL for messaging service. Currently, only MS Teams is supported.",
+                    "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                     "hidden": true
                 },
                 "multiqc_config": {
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
index 1d5a682d..24f02ded 100644
--- a/workflows/smrnaseq.nf
+++ b/workflows/smrnaseq.nf
@@ -82,7 +82,7 @@ workflow SMRNASEQ {
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique().collectFile(name: 'collated_versions.yml')
+        ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml')
     )
 
     //
@@ -102,12 +102,11 @@ workflow SMRNASEQ {
 
     MULTIQC (
         ch_multiqc_files.collect(),
-        ch_multiqc_config.collect().ifEmpty([]),
-        ch_multiqc_custom_config.collect().ifEmpty([]),
-        ch_multiqc_logo.collect().ifEmpty([])
+        ch_multiqc_config.toList(),
+        ch_multiqc_custom_config.toList(),
+        ch_multiqc_logo.toList()
     )
     multiqc_report = MULTIQC.out.report.toList()
-    ch_versions    = ch_versions.mix(MULTIQC.out.versions)
 }
 
 /*
@@ -122,7 +121,7 @@ workflow.onComplete {
     }
     NfcoreTemplate.summary(workflow, params, log)
     if (params.hook_url) {
-        NfcoreTemplate.adaptivecard(workflow, params, summary_params, projectDir, log)
+        NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
     }
 }
 

From e29f9cc290dbdf11de807e4ba8884d0256f37b31 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 19 Dec 2022 12:09:16 +0000
Subject: [PATCH 11/32] Template update for nf-core/tools version 2.7.2

---
 .github/workflows/fix-linting.yml             |  4 +-
 .github/workflows/linting_comment.yml         |  2 +-
 lib/WorkflowMain.groovy                       |  2 +-
 modules.json                                  |  6 +-
 modules/local/samplesheet_check.nf            |  2 +-
 .../custom/dumpsoftwareversions/main.nf       |  2 +-
 .../templates/dumpsoftwareversions.py         | 99 ++++++++++---------
 modules/nf-core/fastqc/main.nf                | 40 +++-----
 modules/nf-core/multiqc/main.nf               |  2 +-
 nextflow.config                               |  3 -
 nextflow_schema.json                          |  6 --
 workflows/smrnaseq.nf                         |  2 +-
 12 files changed, 82 insertions(+), 88 deletions(-)
 mode change 100644 => 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py

diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 4fe16754..ae6a0d7b 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "name=result::pass" >> $GITHUB_OUTPUT
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "name=result::fail" >> $GITHUB_OUTPUT
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 39635186..0bbcd30f 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 6cbc7987..d5372d8c 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -72,7 +72,7 @@ class WorkflowMain {
         NfcoreTemplate.checkConfigProvided(workflow, log)
 
         // Check that conda channels are set-up correctly
-        if (params.enable_conda) {
+        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
             Utils.checkCondaChannels(log)
         }
 
diff --git a/modules.json b/modules.json
index 574bc334..6a70e5a9 100644
--- a/modules.json
+++ b/modules.json
@@ -7,17 +7,17 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index d9a84b5e..94247c70 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -2,7 +2,7 @@ process SAMPLESHEET_CHECK {
     tag "$samplesheet"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    conda "conda-forge::python=3.8.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.8.3' :
         'quay.io/biocontainers/python:3.8.3' }"
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index cebb6e05..3df21765 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
+    conda "bioconda::multiqc=1.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
         'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
old mode 100644
new mode 100755
index 787bdb7b..e55b8d43
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -1,5 +1,9 @@
 #!/usr/bin/env python
 
+
+"""Provide functions to merge multiple versions.yml files."""
+
+
 import platform
 from textwrap import dedent
 
@@ -7,6 +11,7 @@
 
 
 def _make_versions_html(versions):
+    """Generate a tabular HTML output of all versions for MultiQC."""
     html = [
         dedent(
             """\\
@@ -45,47 +50,53 @@ def _make_versions_html(versions):
     return "\\n".join(html)
 
 
-versions_this_module = {}
-versions_this_module["${task.process}"] = {
-    "python": platform.python_version(),
-    "yaml": yaml.__version__,
-}
-
-with open("$versions") as f:
-    versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
-
-# aggregate versions by the module name (derived from fully-qualified process name)
-versions_by_module = {}
-for process, process_versions in versions_by_process.items():
-    module = process.split(":")[-1]
-    try:
-        if versions_by_module[module] != process_versions:
-            raise AssertionError(
-                "We assume that software versions are the same between all modules. "
-                "If you see this error-message it means you discovered an edge-case "
-                "and should open an issue in nf-core/tools. "
-            )
-    except KeyError:
-        versions_by_module[module] = process_versions
-
-versions_by_module["Workflow"] = {
-    "Nextflow": "$workflow.nextflow.version",
-    "$workflow.manifest.name": "$workflow.manifest.version",
-}
-
-versions_mqc = {
-    "id": "software_versions",
-    "section_name": "${workflow.manifest.name} Software Versions",
-    "section_href": "https://github.com/${workflow.manifest.name}",
-    "plot_type": "html",
-    "description": "are collected at run time from the software output.",
-    "data": _make_versions_html(versions_by_module),
-}
-
-with open("software_versions.yml", "w") as f:
-    yaml.dump(versions_by_module, f, default_flow_style=False)
-with open("software_versions_mqc.yml", "w") as f:
-    yaml.dump(versions_mqc, f, default_flow_style=False)
-
-with open("versions.yml", "w") as f:
-    yaml.dump(versions_this_module, f, default_flow_style=False)
+def main():
+    """Load all version files and generate merged output."""
+    versions_this_module = {}
+    versions_this_module["${task.process}"] = {
+        "python": platform.python_version(),
+        "yaml": yaml.__version__,
+    }
+
+    with open("$versions") as f:
+        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
+
+    # aggregate versions by the module name (derived from fully-qualified process name)
+    versions_by_module = {}
+    for process, process_versions in versions_by_process.items():
+        module = process.split(":")[-1]
+        try:
+            if versions_by_module[module] != process_versions:
+                raise AssertionError(
+                    "We assume that software versions are the same between all modules. "
+                    "If you see this error-message it means you discovered an edge-case "
+                    "and should open an issue in nf-core/tools. "
+                )
+        except KeyError:
+            versions_by_module[module] = process_versions
+
+    versions_by_module["Workflow"] = {
+        "Nextflow": "$workflow.nextflow.version",
+        "$workflow.manifest.name": "$workflow.manifest.version",
+    }
+
+    versions_mqc = {
+        "id": "software_versions",
+        "section_name": "${workflow.manifest.name} Software Versions",
+        "section_href": "https://github.com/${workflow.manifest.name}",
+        "plot_type": "html",
+        "description": "are collected at run time from the software output.",
+        "data": _make_versions_html(versions_by_module),
+    }
+
+    with open("software_versions.yml", "w") as f:
+        yaml.dump(versions_by_module, f, default_flow_style=False)
+    with open("software_versions_mqc.yml", "w") as f:
+        yaml.dump(versions_mqc, f, default_flow_style=False)
+
+    with open("versions.yml", "w") as f:
+        yaml.dump(versions_this_module, f, default_flow_style=False)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 05730368..9ae58381 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -2,7 +2,7 @@ process FASTQC {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
+    conda "bioconda::fastqc=0.11.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
         'quay.io/biocontainers/fastqc:0.11.9--0' }"
@@ -20,30 +20,22 @@ process FASTQC {
 
     script:
     def args = task.ext.args ?: ''
-    // Add soft-links to original FastQs for consistent naming in pipeline
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if (meta.single_end) {
-        """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
-        fastqc $args --threads $task.cpus ${prefix}.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        END_VERSIONS
-        """
-    } else {
-        """
-        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
-        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
-        fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        END_VERSIONS
-        """
-    }
+    // Make list of old name and new name pairs to use for renaming in the bash while loop
+    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
+    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+    """
+    printf "%s %s\\n" $rename_to | while read old_name new_name; do
+        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
+    done
+    fastqc $args --threads $task.cpus $renamed_files
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index a8159a57..68f66bea 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -1,7 +1,7 @@
 process MULTIQC {
     label 'process_single'
 
-    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
+    conda "bioconda::multiqc=1.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
         'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
diff --git a/nextflow.config b/nextflow.config
index 07b9d56f..4a87aa48 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -39,7 +39,6 @@ params {
     validate_params            = true
     show_hidden_params         = false
     schema_ignore_params       = 'genomes'
-    enable_conda               = false
 
 
     // Config options
@@ -81,7 +80,6 @@ try {
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
-        params.enable_conda    = true
         conda.enabled          = true
         docker.enabled         = false
         singularity.enabled    = false
@@ -90,7 +88,6 @@ profiles {
         charliecloud.enabled   = false
     }
     mamba {
-        params.enable_conda    = true
         conda.enabled          = true
         conda.useMamba         = true
         docker.enabled         = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 4b6dbf49..f8d98d8c 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -263,12 +263,6 @@
                     "description": "Show all params when using `--help`",
                     "hidden": true,
                     "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "enable_conda": {
-                    "type": "boolean",
-                    "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-bacon"
                 }
             }
         }
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
index 24f02ded..01491244 100644
--- a/workflows/smrnaseq.nf
+++ b/workflows/smrnaseq.nf
@@ -82,7 +82,7 @@ workflow SMRNASEQ {
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml')
+        ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
 
     //

From 65d04a4d9683b1c52b0b541186a89d386e20047a Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Sat, 4 Feb 2023 13:27:44 +0000
Subject: [PATCH 12/32] Update modules

---
 modules.json                                  | 50 ++++++-------------
 .../templates/dumpsoftwareversions.py         | 49 ------------------
 modules/nf-core/fastp/main.nf                 |  2 +-
 modules/nf-core/fastqc/main.nf                |  3 --
 modules/nf-core/multiqc/main.nf               |  6 +--
 modules/nf-core/samtools/flagstat/main.nf     |  6 +--
 modules/nf-core/samtools/idxstats/main.nf     |  8 +--
 modules/nf-core/samtools/index/main.nf        |  6 +--
 modules/nf-core/samtools/sort/main.nf         |  6 +--
 9 files changed, 31 insertions(+), 105 deletions(-)

diff --git a/modules.json b/modules.json
index 06119514..de67a7e7 100644
--- a/modules.json
+++ b/modules.json
@@ -12,65 +12,43 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0"
-                    },
-                    "fastp": {
-                        "branch": "master",
-                        "git_sha": "1e49f31e93c56a3832833eef90a02d3cde5a3f7e"
-                    },
-                    "custom/dumpsoftwareversions": {
-                        "branch": "master",
-                        "git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "1e49f31e93c56a3832833eef90a02d3cde5a3f7e"
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "f6a11408536fbee6cbea1f5977605011873de3ca"
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
-                    },
-                    "samtools/flagstat": {
-                        "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
-                    },
-                    "samtools/idxstats": {
-                        "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
-                    },
-                    "samtools/index": {
-                        "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
-                    },
-                    "samtools/sort": {
-                        "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
-                    },
-                    "samtools/stats": {
-                        "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
+                        "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": ["modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index 5b34099f..da033408 100755
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -1,10 +1,6 @@
 #!/usr/bin/env python
 
 
-"""Provide functions to merge multiple versions.yml files."""
-
-
-
 """Provide functions to merge multiple versions.yml files."""
 
 
@@ -14,7 +10,6 @@
 
 
 def _make_versions_html(versions):
-    """Generate a tabular HTML output of all versions for MultiQC."""
     """Generate a tabular HTML output of all versions for MultiQC."""
     html = [
         dedent(
@@ -54,13 +49,6 @@ def _make_versions_html(versions):
     return "\\n".join(html)
 
 
-def main():
-    """Load all version files and generate merged output."""
-    versions_this_module = {}
-    versions_this_module["${task.process}"] = {
-        "python": platform.python_version(),
-        "yaml": yaml.__version__,
-    }
 def main():
     """Load all version files and generate merged output."""
     versions_this_module = {}
@@ -69,26 +57,11 @@ def main():
         "yaml": yaml.__version__,
     }
 
-    with open("$versions") as f:
-        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
     with open("$versions") as f:
         versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
 
     # aggregate versions by the module name (derived from fully-qualified process name)
     versions_by_module = {}
-    for process, process_versions in versions_by_process.items():
-        module = process.split(":")[-1]
-        try:
-            if versions_by_module[module] != process_versions:
-                raise AssertionError(
-                    "We assume that software versions are the same between all modules. "
-                    "If you see this error-message it means you discovered an edge-case "
-                    "and should open an issue in nf-core/tools. "
-                )
-        except KeyError:
-            versions_by_module[module] = process_versions
-    # aggregate versions by the module name (derived from fully-qualified process name)
-    versions_by_module = {}
     for process, process_versions in versions_by_process.items():
         module = process.split(":")[-1]
         try:
@@ -105,19 +78,7 @@ def main():
         "Nextflow": "$workflow.nextflow.version",
         "$workflow.manifest.name": "$workflow.manifest.version",
     }
-    versions_by_module["Workflow"] = {
-        "Nextflow": "$workflow.nextflow.version",
-        "$workflow.manifest.name": "$workflow.manifest.version",
-    }
 
-    versions_mqc = {
-        "id": "software_versions",
-        "section_name": "${workflow.manifest.name} Software Versions",
-        "section_href": "https://github.com/${workflow.manifest.name}",
-        "plot_type": "html",
-        "description": "are collected at run time from the software output.",
-        "data": _make_versions_html(versions_by_module),
-    }
     versions_mqc = {
         "id": "software_versions",
         "section_name": "${workflow.manifest.name} Software Versions",
@@ -127,10 +88,6 @@ def main():
         "data": _make_versions_html(versions_by_module),
     }
 
-    with open("software_versions.yml", "w") as f:
-        yaml.dump(versions_by_module, f, default_flow_style=False)
-    with open("software_versions_mqc.yml", "w") as f:
-        yaml.dump(versions_mqc, f, default_flow_style=False)
     with open("software_versions.yml", "w") as f:
         yaml.dump(versions_by_module, f, default_flow_style=False)
     with open("software_versions_mqc.yml", "w") as f:
@@ -138,12 +95,6 @@ def main():
 
     with open("versions.yml", "w") as f:
         yaml.dump(versions_this_module, f, default_flow_style=False)
-    with open("versions.yml", "w") as f:
-        yaml.dump(versions_this_module, f, default_flow_style=False)
-
-
-if __name__ == "__main__":
-    main()
 
 
 if __name__ == "__main__":
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
index 207258ad..e1ed9288 100644
--- a/modules/nf-core/fastp/main.nf
+++ b/modules/nf-core/fastp/main.nf
@@ -2,7 +2,7 @@ process FASTP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null)
+    conda "bioconda::fastp=0.23.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
         'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 510978af..9ae58381 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -30,9 +30,6 @@ process FASTQC {
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
     done
     fastqc $args --threads $task.cpus $renamed_files
-    """
-    printf "%s\\n" $reads | while read f; do ln -s \$f ${prefix}_\$(basename \$f) ; done
-    fastqc $args --threads $task.cpus ${prefix}_*
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 68f66bea..4b604749 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -1,10 +1,10 @@
 process MULTIQC {
     label 'process_single'
 
-    conda "bioconda::multiqc=1.13"
+    conda "bioconda::multiqc=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
index c3152aca..2120cd7d 100644
--- a/modules/nf-core/samtools/flagstat/main.nf
+++ b/modules/nf-core/samtools/flagstat/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    conda "bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
+        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf
index 87618e5f..a7b87d8b 100644
--- a/modules/nf-core/samtools/idxstats/main.nf
+++ b/modules/nf-core/samtools/idxstats/main.nf
@@ -1,11 +1,11 @@
 process SAMTOOLS_IDXSTATS {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    conda "bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
+        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
index e04e63e8..8b95687a 100644
--- a/modules/nf-core/samtools/index/main.nf
+++ b/modules/nf-core/samtools/index/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_INDEX {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    conda "bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
+        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index ab7f1cca..84c167cd 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_SORT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    conda "bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
+        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
 
     input:
     tuple val(meta), path(bam)

From bb8c60374c4d3e5f4846c5e02ad08ae13a941502 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Sat, 4 Feb 2023 13:31:00 +0000
Subject: [PATCH 13/32] Fix prettier

---
 CHANGELOG.md  | 2 +-
 docs/usage.md | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 79e4e5cc..6e73c128 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,7 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Dev
 
-* Updated FASTP module to allow direct addition of adapter_fasta file to it
+- Updated FASTP module to allow direct addition of adapter_fasta file to it
 
 ## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-20 Maroon Tin Dalmatian
 
diff --git a/docs/usage.md b/docs/usage.md
index 056c0b77..f0027bcf 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -139,7 +139,7 @@ This version number will be logged in reports when you run the pipeline, so that
 The `bin` directory contains some scripts used by the pipeline which may also be run manually:
 
 - `edgeR_miRBase.r`: R script using for processing reads counts of mature miRNAs and miRNA precursors (hairpins).
-This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
+  This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
 
 ## Core Nextflow arguments
 

From bba81497cbde8b656c73e3657f102bf58c014012 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Tue, 7 Feb 2023 20:06:55 +0000
Subject: [PATCH 14/32] Fix black

---
 assets/methods_description_template.yml | 2 --
 bin/check_samplesheet.py                | 1 -
 modules/nf-core/cat/fastq/main.nf       | 2 +-
 modules/nf-core/samtools/stats/main.nf  | 6 +++---
 nextflow.config                         | 1 -
 5 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
index 247628aa..1f05424e 100644
--- a/assets/methods_description_template.yml
+++ b/assets/methods_description_template.yml
@@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/smrnaseq Methods Description"
 section_href: "https://github.com/nf-core/smrnaseq"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
-## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
   <p>Data was processed using nf-core/smrnaseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index 24252b4b..757199ac 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -50,7 +50,6 @@ def check_samplesheet(file_in, file_out):
 
     sample_mapping_dict = {}
     with open(file_in, "r") as fin:
-
         ## Check header
         MIN_COLS = 2
         HEADER = ["sample", "fastq_1"]
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
index 4fa365d3..8a0b5600 100644
--- a/modules/nf-core/cat/fastq/main.nf
+++ b/modules/nf-core/cat/fastq/main.nf
@@ -2,7 +2,7 @@ process CAT_FASTQ {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'ubuntu:20.04' }"
diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf
index 9b0c3867..0a2a3640 100644
--- a/modules/nf-core/samtools/stats/main.nf
+++ b/modules/nf-core/samtools/stats/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_STATS {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    conda "bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
+        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
 
     input:
     tuple val(meta), path(input), path(input_index)
diff --git a/nextflow.config b/nextflow.config
index 80a6263f..fbe64350 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -74,7 +74,6 @@ params {
     validate_params            = true
     show_hidden_params         = false
     schema_ignore_params       = 'genomes'
-    enable_conda               = false
 
 
     // Config options

From c3a4201de91142f54fc2318c08bc9a4cddc26ccc Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Tue, 7 Feb 2023 20:36:17 +0000
Subject: [PATCH 15/32] Fix Conda directives

---
 modules/local/blat_mirna.nf              | 2 +-
 modules/local/bowtie_contaminants.nf     | 2 +-
 modules/local/bowtie_genome.nf           | 2 +-
 modules/local/bowtie_map_contaminants.nf | 2 +-
 modules/local/bowtie_map_mirna.nf        | 2 +-
 modules/local/bowtie_mirna.nf            | 2 +-
 modules/local/datatable_merge.nf         | 2 +-
 modules/local/edger_qc.nf                | 2 +-
 modules/local/filter_stats.nf            | 2 +-
 modules/local/format_fasta_mirna.nf      | 2 +-
 modules/local/mirdeep2_mapper.nf         | 2 +-
 modules/local/mirdeep2_prepare.nf        | 2 +-
 modules/local/mirdeep2_run.nf            | 2 +-
 modules/local/mirtop_quant.nf            | 2 +-
 modules/local/mirtrace.nf                | 2 +-
 modules/local/parse_fasta_mirna.nf       | 2 +-
 modules/local/seqcluster_collapse.nf     | 2 +-
 workflows/smrnaseq.nf                    | 2 ++
 18 files changed, 19 insertions(+), 17 deletions(-)

diff --git a/modules/local/blat_mirna.nf b/modules/local/blat_mirna.nf
index 2b50d7db..198e001c 100644
--- a/modules/local/blat_mirna.nf
+++ b/modules/local/blat_mirna.nf
@@ -2,7 +2,7 @@ process BLAT_MIRNA {
     tag "$fasta"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::blat=36' : null)
+    conda 'bioconda::blat=36'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/blat:36--0' :
         'quay.io/biocontainers/blat:36--0' }"
diff --git a/modules/local/bowtie_contaminants.nf b/modules/local/bowtie_contaminants.nf
index 1145b56f..a68b8530 100644
--- a/modules/local/bowtie_contaminants.nf
+++ b/modules/local/bowtie_contaminants.nf
@@ -1,7 +1,7 @@
 process INDEX_CONTAMINANTS {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bowtie2=2.4.5' : null)
+    conda 'bowtie2=2.4.5'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bowtie2:2.4.5--py39hd2f7db1_2' :
         'quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2'}"
diff --git a/modules/local/bowtie_genome.nf b/modules/local/bowtie_genome.nf
index 1fb38551..1405467a 100644
--- a/modules/local/bowtie_genome.nf
+++ b/modules/local/bowtie_genome.nf
@@ -2,7 +2,7 @@ process INDEX_GENOME {
     tag "$fasta"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bowtie=1.3.1-4' : null)
+    conda 'bioconda::bowtie=1.3.1-4'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bowtie%3A1.3.1--py39hd400a0c_2' :
         'quay.io/biocontainers/bowtie:1.3.1--py310h4070885_4' }"
diff --git a/modules/local/bowtie_map_contaminants.nf b/modules/local/bowtie_map_contaminants.nf
index bbfb66fd..09ad0162 100644
--- a/modules/local/bowtie_map_contaminants.nf
+++ b/modules/local/bowtie_map_contaminants.nf
@@ -1,7 +1,7 @@
 process BOWTIE_MAP_CONTAMINANTS {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bowtie2=2.4.5' : null)
+    conda 'bowtie2=2.4.5'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bowtie2:2.4.5--py39hd2f7db1_2' :
         'quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2' }"
diff --git a/modules/local/bowtie_map_mirna.nf b/modules/local/bowtie_map_mirna.nf
index 82d7acf8..8202838f 100644
--- a/modules/local/bowtie_map_mirna.nf
+++ b/modules/local/bowtie_map_mirna.nf
@@ -2,7 +2,7 @@ process BOWTIE_MAP_SEQ {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bowtie=1.3.0-2 bioconda::samtools=1.13' : null)
+    conda 'bowtie=1.3.0-2 bioconda::samtools=1.13'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0' :
         'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0' }"
diff --git a/modules/local/bowtie_mirna.nf b/modules/local/bowtie_mirna.nf
index 0be5888b..601c9f43 100644
--- a/modules/local/bowtie_mirna.nf
+++ b/modules/local/bowtie_mirna.nf
@@ -1,7 +1,7 @@
 process INDEX_MIRNA {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bowtie=1.3.0-2' : null)
+    conda 'bioconda::bowtie=1.3.0-2'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bowtie%3A1.3.1--py39hd400a0c_2' :
         'quay.io/biocontainers/bowtie:1.3.1--py310h4070885_4' }"
diff --git a/modules/local/datatable_merge.nf b/modules/local/datatable_merge.nf
index 8a1ed3b5..5b238c06 100644
--- a/modules/local/datatable_merge.nf
+++ b/modules/local/datatable_merge.nf
@@ -1,7 +1,7 @@
 process TABLE_MERGE {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'conda-base::r-data.table=1.12.2' : null)
+    conda 'conda-base::r-data.table=1.12.2'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/r-data.table:1.12.2' :
         'quay.io/biocontainers/r-data.table:1.12.2' }"
diff --git a/modules/local/edger_qc.nf b/modules/local/edger_qc.nf
index 023f70be..0d8efe64 100644
--- a/modules/local/edger_qc.nf
+++ b/modules/local/edger_qc.nf
@@ -1,7 +1,7 @@
 process EDGER_QC {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bioconductor-limma=3.50.0 bioconda::bioconductor-edger=3.36.0 conda-forge::r-data.table=1.14.2 conda-forge::r-gplots=3.1.1 conda-forge::r-statmod=1.4.36' : null)
+    conda 'bioconda::bioconductor-limma=3.50.0 bioconda::bioconductor-edger=3.36.0 conda-forge::r-data.table=1.14.2 conda-forge::r-gplots=3.1.1 conda-forge::r-statmod=1.4.36'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:709335c37934db1b481054cbec637c6e5b5971cb-0' :
         'quay.io/biocontainers/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:709335c37934db1b481054cbec637c6e5b5971cb-0' }"
diff --git a/modules/local/filter_stats.nf b/modules/local/filter_stats.nf
index 4d94d9b1..c9336f22 100644
--- a/modules/local/filter_stats.nf
+++ b/modules/local/filter_stats.nf
@@ -1,7 +1,7 @@
 process FILTER_STATS {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bowtie2=2.4.5' : null)
+    conda 'bowtie2=2.4.5'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bowtie2:2.4.5--py39hd2f7db1_2' :
         'quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2' }"
diff --git a/modules/local/format_fasta_mirna.nf b/modules/local/format_fasta_mirna.nf
index d19901fd..2c39c0aa 100644
--- a/modules/local/format_fasta_mirna.nf
+++ b/modules/local/format_fasta_mirna.nf
@@ -4,7 +4,7 @@ process FORMAT_FASTA_MIRNA {
     tag "$fasta"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::fastx_toolkit=0.0.14-9' : null)
+    conda 'bioconda::fastx_toolkit=0.0.14-9'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fastx_toolkit:0.0.14--he1b5a44_8' :
         'quay.io/biocontainers/fastx_toolkit:0.0.14--he1b5a44_8' }"
diff --git a/modules/local/mirdeep2_mapper.nf b/modules/local/mirdeep2_mapper.nf
index 7d90712b..2293ef87 100644
--- a/modules/local/mirdeep2_mapper.nf
+++ b/modules/local/mirdeep2_mapper.nf
@@ -4,7 +4,7 @@ process MIRDEEP2_MAPPER {
     label 'process_medium'
     tag "$meta.id"
 
-    conda (params.enable_conda ? 'bioconda::mirdeep2=2.0.1' : null)
+    conda 'bioconda::mirdeep2=2.0.1'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mirdeep2:2.0.1.3--hdfd78af_1' :
         'quay.io/biocontainers/mirdeep2:2.0.1.3--hdfd78af_1' }"
diff --git a/modules/local/mirdeep2_prepare.nf b/modules/local/mirdeep2_prepare.nf
index 9fcc2ed5..3d117d4a 100644
--- a/modules/local/mirdeep2_prepare.nf
+++ b/modules/local/mirdeep2_prepare.nf
@@ -3,7 +3,7 @@ process MIRDEEP2_PIGZ {
     tag "$meta.id"
 
     // TODO maybe create a mulled container and uncompress within mirdeep2_mapper?
-    conda (params.enable_conda ? 'bioconda::bioconvert=0.4.3' : null)
+    conda 'bioconda::bioconvert=0.4.3'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconvert:0.4.3--py_0' :
         'quay.io/biocontainers/bioconvert:0.4.3--py_0' }"
diff --git a/modules/local/mirdeep2_run.nf b/modules/local/mirdeep2_run.nf
index ee4cfc0d..2035658c 100644
--- a/modules/local/mirdeep2_run.nf
+++ b/modules/local/mirdeep2_run.nf
@@ -4,7 +4,7 @@ process MIRDEEP2_RUN {
     label 'process_medium'
     errorStrategy 'ignore'
 
-    conda (params.enable_conda ? 'bioconda::mirdeep2=2.0.1' : null)
+    conda 'bioconda::mirdeep2=2.0.1'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mirdeep2:2.0.1.3--hdfd78af_1' :
         'quay.io/biocontainers/mirdeep2:2.0.1.3--hdfd78af_1' }"
diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf
index b6f72a89..c4e76a3c 100644
--- a/modules/local/mirtop_quant.nf
+++ b/modules/local/mirtop_quant.nf
@@ -1,7 +1,7 @@
 process MIRTOP_QUANT {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'mirtop=0.4.25 bioconda::samtools=1.15.1 conda-base::r-base=4.1.1 conda-base::r-data.table=1.14.2' : null)
+    conda 'mirtop=0.4.25 bioconda::samtools=1.15.1 conda-base::r-base=4.1.1 conda-base::r-data.table=1.14.2'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' :
         'quay.io/biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }"
diff --git a/modules/local/mirtrace.nf b/modules/local/mirtrace.nf
index 8683d5ce..8c2102f6 100644
--- a/modules/local/mirtrace.nf
+++ b/modules/local/mirtrace.nf
@@ -1,7 +1,7 @@
 process MIRTRACE_RUN {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::mirtrace=1.0.1' : null)
+    conda 'bioconda::mirtrace=1.0.1'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mirtrace:1.0.1--hdfd78af_1' :
         'quay.io/biocontainers/mirtrace:1.0.1--hdfd78af_1' }"
diff --git a/modules/local/parse_fasta_mirna.nf b/modules/local/parse_fasta_mirna.nf
index e09242eb..5418f597 100644
--- a/modules/local/parse_fasta_mirna.nf
+++ b/modules/local/parse_fasta_mirna.nf
@@ -1,7 +1,7 @@
 process PARSE_FASTA_MIRNA {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::seqkit=2.3.1' : null)
+    conda 'bioconda::seqkit=2.3.1'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/seqkit:2.3.1--h9ee0642_0' :
         'quay.io/biocontainers/seqkit:2.3.1--h9ee0642_0' }"
diff --git a/modules/local/seqcluster_collapse.nf b/modules/local/seqcluster_collapse.nf
index 46239775..36645ee1 100644
--- a/modules/local/seqcluster_collapse.nf
+++ b/modules/local/seqcluster_collapse.nf
@@ -2,7 +2,7 @@ process SEQCLUSTER_SEQUENCES {
     label 'process_medium'
     tag "$meta.id"
 
-    conda (params.enable_conda ? 'bioconda::seqcluster=1.2.9-0' : null)
+    conda 'bioconda::seqcluster=1.2.9-0'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/seqcluster:1.2.9--pyh5e36f6f_0' :
         'quay.io/biocontainers/seqcluster:1.2.8--pyh5e36f6f_0' }"
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
index 61e87545..3176aead 100644
--- a/workflows/smrnaseq.nf
+++ b/workflows/smrnaseq.nf
@@ -238,8 +238,10 @@ workflow SMRNASEQ {
         ch_multiqc_logo.toList()
     )
     multiqc_report = MULTIQC.out.report.toList()
+    }
 }
 
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     COMPLETION EMAIL AND SUMMARY

From 33de978788ed4dfdf0d4f51aa15ce6d3fce6f64a Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Tue, 7 Feb 2023 21:38:15 +0100
Subject: [PATCH 16/32] Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
---
 conf/modules.config | 2 +-
 nextflow.config     | 5 +----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 64d851f6..0c5365fb 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -104,7 +104,7 @@ if (!params.skip_fastp) {
             params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
             params.fastp_min_length > 0    ? "-l ${params.fastp_min_length}" : "",
             params.fastp_max_length > 0    ? "--max_len1 ${params.fastp_max_length}" : "",
-            params.three_prime_adapter == null ?  '' : "--adapter_sequence ${params.three_prime_adapter}",
+            params.three_prime_adapter == null ?  '' : "--adapter_sequence ${params.three_prime_adapter}"
         ].join(" ").trim()
             publishDir = [
                 [
diff --git a/nextflow.config b/nextflow.config
index fbe64350..1df2f6de 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -141,9 +141,6 @@ profiles {
     arm {
         docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
-    arm {
-        docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
-    }
     singularity {
         singularity.enabled     = true
         singularity.autoMounts  = true
@@ -224,7 +221,7 @@ dag {
 
 manifest {
     name            = 'nf-core/smrnaseq'
-    author          = """P. Ewels, C. Wang, R. Hammarén, L. Pantano"""
+    author          = """P. Ewels, C. Wang, R. Hammarén, L. Pantano, A. Peltzer"""
     homePage        = 'https://github.com/nf-core/smrnaseq'
     description     = """Small RNA-Seq Best Practice Analysis Pipeline."""
     mainScript      = 'main.nf'

From f81ddb4871882c32e92b9172efbf85295962697c Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Tue, 7 Feb 2023 20:41:20 +0000
Subject: [PATCH 17/32] Redid licence, to match lint

---
 LICENSE | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/LICENSE b/LICENSE
index 499134b1..d6a83450 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) P. Ewels, C. Wang, R. Hammarén, L. Pantano
+Copyright (c) P. Ewels, C. Wang, R. Hammarén, L. Pantano, A. Peltzer
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

From 8810b086b2956dc25187a915e1c468b48d1d063b Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Fri, 17 Feb 2023 22:36:39 +0100
Subject: [PATCH 18/32] Fix for edgeR QC

Co-authored-by: Sean Corbett @sean-at-tessera
---
 bin/edgeR_miRBase.r | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/edgeR_miRBase.r b/bin/edgeR_miRBase.r
index d6647a31..5be691fc 100755
--- a/bin/edgeR_miRBase.r
+++ b/bin/edgeR_miRBase.r
@@ -43,7 +43,7 @@ for (i in 1:2) {
     # Only subset if at least one sample is remaining
     nr_keep <- sum(row_sub)
     if (nr_keep > 0){
-        data<-data[!row_sub,]
+        data<-data[!row_sub,, drop=FALSE]
     }
     #Also check for colSums > 0, otherwise DGEList will fail if samples have entirely colSum == 0 #Fixes #134
     drop_colsum_zero <- (colSums(data, na.rm=T) != 0) # T if colSum is not 0, F otherwise

From 1b1bea521fb59dfec64e09783ecab191d52c0832 Mon Sep 17 00:00:00 2001
From: Barry digby <b.digby237@gmail.com>
Date: Sat, 18 Feb 2023 15:22:38 +0000
Subject: [PATCH 19/32] FASTP fix

---
 subworkflows/nf-core/fastqc_fastp.nf | 2 +-
 workflows/smrnaseq.nf                | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/subworkflows/nf-core/fastqc_fastp.nf b/subworkflows/nf-core/fastqc_fastp.nf
index 5cec3149..5eb2b545 100644
--- a/subworkflows/nf-core/fastqc_fastp.nf
+++ b/subworkflows/nf-core/fastqc_fastp.nf
@@ -28,7 +28,7 @@ String getFastpAdapterSequence(json_file){
 workflow FASTQC_FASTP {
     take:
     reads             // channel: [ val(meta), [ reads ] ]
-    adapter_list      // String [path/to/adapters.fa]
+    adapter_list      // channel: [ path/to/adapters.fa ]
     save_trimmed_fail //   value: boolean
     save_merged       //   value: boolean
 
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
index 2a63ee64..dd52ea2f 100644
--- a/workflows/smrnaseq.nf
+++ b/workflows/smrnaseq.nf
@@ -38,7 +38,7 @@ ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config
 ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
 ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
 ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-ch_fastp_adapters          = Channel.fromPath(params.fastp_known_mirna_adapters, checkIfExists: true)
+ch_fastp_adapters          = Channel.fromPath(params.fastp_known_mirna_adapters, checkIfExists: true).collect() // collect to consume for all incoming samples to FASTP
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -150,7 +150,7 @@ workflow SMRNASEQ {
 
     } else{
         //TODO - rob? :-)
-        
+
     }
 
 

From 2ceaa97c61b29bc0377a1da66fb63888fa4e5726 Mon Sep 17 00:00:00 2001
From: Denis O'Meally <omeally@gmail.com>
Date: Sun, 19 Feb 2023 20:08:56 -0800
Subject: [PATCH 20/32] mirtrace fix

---
 modules/local/mirtrace.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/local/mirtrace.nf b/modules/local/mirtrace.nf
index 8c2102f6..90dbd5f1 100644
--- a/modules/local/mirtrace.nf
+++ b/modules/local/mirtrace.nf
@@ -21,6 +21,7 @@ process MIRTRACE_RUN {
     def primer = meta.adapter ? "--adapter ${meta.adapter}" : ""
     def protocol = params.protocol == 'custom' ? '' : "--protocol $params.protocol"
     def java_mem = ''
+    def prefix = "${meta.id}"
     if(task.memory){
         tmem = task.memory.toBytes()
         java_mem = "-Xms${tmem} -Xmx${tmem}"
@@ -30,7 +31,7 @@ process MIRTRACE_RUN {
     for i in $reads
     do
         path=\$(realpath \${i})
-        prefix=\$(echo \${i} | sed -e 's/.gz//' -e 's/.fastq//' -e 's/.fq//' -e 's/_val_1//' -e 's/_trimmed//' -e 's/_R1//' -e 's/.R1//')
+        prefix=$prefix
         echo \$path","\$prefix
     done > mirtrace_config
 

From 922ba8aa8dc25ca22ede14d801d6a2bd7c2d60d2 Mon Sep 17 00:00:00 2001
From: Denis OMeally <omeally@gmail.com>
Date: Mon, 20 Feb 2023 12:30:25 -0800
Subject: [PATCH 21/32] Update CHANGELOG.md

Fix #220
---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6a881780..953f295a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Dev
 
+- [[#220](https://github.com/nf-core/smrnaseq/issues/220)] - Fixed an issue where miRTrace reports fastq basename instead of sample ID
 - [[#208](https://github.com/nf-core/smrnaseq/issues/208)] - Fixed usability of `--skip_qc` parameter
 - Updated FASTP module to allow direct addition of adapter_fasta file to it
 - [[#205](https://github.com/nf-core/smrnaseq/issues/205)] - Fix mirTrace Report to be a single report again instead of per sample reports

From fb26c3dcdaf5df3e3866b0a14f18a5cccc84c467 Mon Sep 17 00:00:00 2001
From: MagdalenaZZ <mzarowiecki@gmail.com>
Date: Thu, 30 Mar 2023 15:37:26 +0100
Subject: [PATCH 22/32] Update check_samplesheet.py

Change eprint to print_error on line 60, to remain consistent with error messaging throughout, and to remove dependency on eprint.
---
 bin/check_samplesheet.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index 24252b4b..2ed13416 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -57,7 +57,7 @@ def check_samplesheet(file_in, file_out):
         header = [x.strip('"') for x in fin.readline().strip().split(",")]
         if any([item not in header for item in HEADER]):
             missing = [item for item in HEADER if item not in header]
-            eprint("ERROR: Please check samplesheet header. Missing columns: '{}'".format(",".join(missing)))
+            print_error("ERROR: Please check samplesheet header. Missing columns: '{}'".format(",".join(missing)))
             sys.exit(1)
 
         ## Check sample entries

From b7321042e9bf30429add9457a899c9c1251647d2 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Tue, 4 Apr 2023 14:23:30 +0200
Subject: [PATCH 23/32] Update CHANGELOG.md

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 69a23be8..d0cd1f34 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## dev
+
+- Fix issue in Samplesheet checking
+
 ## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-25 Maroon Tin Dalmatian
 
 ### Enhancements & fixes

From b9a7fcedef61cb5588afca4a1aaec50097a07750 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 19 Apr 2023 14:05:46 +0100
Subject: [PATCH 24/32] Update all nf-core/modules

---
 modules.json                                       | 14 +++++++-------
 .../nf-core/custom/dumpsoftwareversions/main.nf    |  6 +++---
 .../templates/dumpsoftwareversions.py              |  0
 modules/nf-core/fastp/main.nf                      |  1 -
 modules/nf-core/fastp/meta.yml                     |  2 +-
 modules/nf-core/samtools/flagstat/meta.yml         |  2 +-
 modules/nf-core/samtools/idxstats/meta.yml         |  2 +-
 modules/nf-core/samtools/index/meta.yml            |  2 +-
 modules/nf-core/samtools/sort/meta.yml             |  2 +-
 modules/nf-core/samtools/stats/meta.yml            | 14 +++++++-------
 10 files changed, 22 insertions(+), 23 deletions(-)
 mode change 100755 => 100644 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py

diff --git a/modules.json b/modules.json
index de67a7e7..a4d925ab 100644
--- a/modules.json
+++ b/modules.json
@@ -12,12 +12,12 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "7101db4432d3268b7fcb5b8f75fa0a022dc5561b",
                         "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "20a508676f40d0fd3f911ac595af91ec845704c4",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
@@ -32,27 +32,27 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
                         "installed_by": ["modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
                         "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 3df21765..800a6099 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "bioconda::multiqc=1.13"
+    conda "bioconda::multiqc=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
 
     input:
     path versions
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
old mode 100755
new mode 100644
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
index e1ed9288..5eeb9b09 100644
--- a/modules/nf-core/fastp/main.nf
+++ b/modules/nf-core/fastp/main.nf
@@ -58,7 +58,6 @@ process FASTP {
         [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
 
         fastp \\
-            --stdout \\
             --in1 ${prefix}.fastq.gz \\
             --out1  ${prefix}.fastp.fastq.gz \\
             --thread $task.cpus \\
diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml
index 6f6fad74..197ea7ca 100644
--- a/modules/nf-core/fastp/meta.yml
+++ b/modules/nf-core/fastp/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: |
         A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
       documentation: https://github.com/OpenGene/fastp
-      doi: https://doi.org/10.1093/bioinformatics/bty560
+      doi: 10.1093/bioinformatics/bty560
       licence: ["MIT"]
 input:
   - meta:
diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml
index 95269063..954225df 100644
--- a/modules/nf-core/samtools/flagstat/meta.yml
+++ b/modules/nf-core/samtools/flagstat/meta.yml
@@ -14,7 +14,7 @@ tools:
         short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
         These files are generated as output by short read aligners like BWA.
       homepage: http://www.htslib.org/
-      documentation: hhttp://www.htslib.org/doc/samtools.html
+      documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
 input:
diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml
index 3710ab88..dda87e1e 100644
--- a/modules/nf-core/samtools/idxstats/meta.yml
+++ b/modules/nf-core/samtools/idxstats/meta.yml
@@ -15,7 +15,7 @@ tools:
         short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
         These files are generated as output by short read aligners like BWA.
       homepage: http://www.htslib.org/
-      documentation: hhttp://www.htslib.org/doc/samtools.html
+      documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
 input:
diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml
index e5cadbc2..8bd2fa6f 100644
--- a/modules/nf-core/samtools/index/meta.yml
+++ b/modules/nf-core/samtools/index/meta.yml
@@ -12,7 +12,7 @@ tools:
         short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
         These files are generated as output by short read aligners like BWA.
       homepage: http://www.htslib.org/
-      documentation: hhttp://www.htslib.org/doc/samtools.html
+      documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
 input:
diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
index 09289751..07328431 100644
--- a/modules/nf-core/samtools/sort/meta.yml
+++ b/modules/nf-core/samtools/sort/meta.yml
@@ -12,7 +12,7 @@ tools:
         short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
         These files are generated as output by short read aligners like BWA.
       homepage: http://www.htslib.org/
-      documentation: hhttp://www.htslib.org/doc/samtools.html
+      documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
 input:
diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml
index cac50b1c..1d68a5d8 100644
--- a/modules/nf-core/samtools/stats/meta.yml
+++ b/modules/nf-core/samtools/stats/meta.yml
@@ -13,7 +13,7 @@ tools:
         short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
         These files are generated as output by short read aligners like BWA.
       homepage: http://www.htslib.org/
-      documentation: hhttp://www.htslib.org/doc/samtools.html
+      documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
 input:
@@ -23,13 +23,13 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - input:
-    type: file
-    description: BAM/CRAM file from alignment
-    pattern: "*.{bam,cram}"
+      type: file
+      description: BAM/CRAM file from alignment
+      pattern: "*.{bam,cram}"
   - input_index:
-    type: file
-    description: BAI/CRAI file from alignment
-    pattern: "*.{bai,crai}"
+      type: file
+      description: BAI/CRAI file from alignment
+      pattern: "*.{bai,crai}"
   - fasta:
       type: optional file
       description: Reference file the CRAM was created with

From 70071d73e09a90f558608d595693858c78ba5049 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 24 Apr 2023 09:31:29 +0100
Subject: [PATCH 25/32] Bump pipeline version to 2.2.0

---
 CHANGELOG.md    | 2 +-
 nextflow.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fc82b1f8..61f0e022 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## Dev
+## [v2.2.0](https://github.com/nf-core/smrnaseq/releases/tag/2.2.0) - 2023-04-25
 
 - [[#220](https://github.com/nf-core/smrnaseq/issues/220)] - Fixed an issue where miRTrace reports fastq basename instead of sample ID
 - [[#208](https://github.com/nf-core/smrnaseq/issues/208)] - Fixed usability of `--skip_qc` parameter
diff --git a/nextflow.config b/nextflow.config
index 1df2f6de..c53e2a86 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -226,7 +226,7 @@ manifest {
     description     = """Small RNA-Seq Best Practice Analysis Pipeline."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '2.1.1dev'
+    version         = '2.2.0'
     doi             = ''
 }
 

From 2625e11d5469ca802a5367c12723c1a8b755a2cd Mon Sep 17 00:00:00 2001
From: Rob Syme <rob.syme@gmail.com>
Date: Mon, 24 Apr 2023 23:40:35 -0400
Subject: [PATCH 26/32] Remove skip_qc parameter

---
 conf/modules.config   |  2 +-
 nextflow.config       |  1 -
 nextflow_schema.json  |  5 -----
 workflows/smrnaseq.nf | 41 +++++++++++++++--------------------------
 4 files changed, 16 insertions(+), 33 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 0c5365fb..8644dd3c 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -87,7 +87,7 @@ process {
     }
 }
 
-if (!(params.skip_fastqc || params.skip_qc)) {
+if (!(params.skip_fastqc)) {
     process {
         withName: '.*:FASTQC_FASTP:FASTQC_.*' {
             ext.args = '--quiet'
diff --git a/nextflow.config b/nextflow.config
index c53e2a86..7b6f2d8e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -36,7 +36,6 @@ params {
     fastp_min_length            = 17
     fastp_known_mirna_adapters  = "$projectDir/assets/known_adapters.fa"
     save_trimmed_fail           = false
-    skip_qc                     = false
     skip_fastqc                 = false
     skip_multiqc                = false
     skip_mirdeep                = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index f6911a15..213199c1 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -249,11 +249,6 @@
             "description": "Switches to skip specific pipeline steps, if desired.",
             "fa_icon": "fas fa-fast-forward",
             "properties": {
-                "skip_qc": {
-                    "type": "boolean",
-                    "fa_icon": "fas fa-fast-forward",
-                    "description": "Skip all QC steps"
-                },
                 "skip_fastqc": {
                     "type": "boolean",
                     "fa_icon": "fas fa-fast-forward",
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
index dd52ea2f..c3aaa55f 100644
--- a/workflows/smrnaseq.nf
+++ b/workflows/smrnaseq.nf
@@ -125,7 +125,6 @@ workflow SMRNASEQ {
     // SUBWORKFLOW: Read QC and trim adapters
     //
 
-    if(!params.skip_qc){
     FASTQC_FASTP (
         ch_cat_fastq,
         ch_fastp_adapters,
@@ -133,28 +132,21 @@ workflow SMRNASEQ {
         false
     )
     ch_versions = ch_versions.mix(FASTQC_FASTP.out.versions)
-    reads_for_mirna = FASTQC_FASTP.out.reads
-
+    ch_reads = FASTQC_FASTP.out.reads
 
     //
     // SUBWORKFLOW: mirtrace QC
     //
-    ch_outputs_for_mirtrace = FASTQC_FASTP.out.adapterseq
+    FASTQC_FASTP.out.adapterseq
     .join( ch_cat_fastq )
     .map { meta, adapterseq, fastq -> [meta + [adapter:adapterseq], fastq] }
     .collect()
+    .set { ch_mitrace_inputs }
 
-    MIRTRACE(ch_outputs_for_mirtrace)
 
+    MIRTRACE(ch_mitrace_inputs)
     ch_versions = ch_versions.mix(MIRTRACE.out.versions.ifEmpty(null))
 
-    } else{
-        //TODO - rob? :-)
-
-    }
-
-
-
 
     //
     // SUBWORKFLOW: remove contaminants from reads
@@ -172,10 +164,8 @@ workflow SMRNASEQ {
             FASTQC_FASTP.out.reads
         )
 
-        reads_for_mirna = CONTAMINANT_FILTER.out.filtered_reads
+        contamination_stats = CONTAMINANT_FILTER.out.filter_stats
         ch_versions = ch_versions.mix(CONTAMINANT_FILTER.out.versions)
-        CONTAMINANT_FILTER.out.filter_stats
-            .set { contamination_stats }
 
     }
 
@@ -183,7 +173,7 @@ workflow SMRNASEQ {
         reference_mature,
         reference_hairpin,
         mirna_gtf,
-        reads_for_mirna
+        CONTAMINANT_FILTER.out.filtered_reads
     )
     ch_versions = ch_versions.mix(MIRNA_QUANT.out.versions.ifEmpty(null))
 
@@ -229,9 +219,8 @@ workflow SMRNASEQ {
         ch_multiqc_files = Channel.empty()
         ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
         ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-
-        ch_multiqc_files = ch_multiqc_files.mix(FASTQC_FASTP.out.fastqc_raw_zip.collect{it[1]}.ifEmpty([])),
-        ch_multiqc_files = ch_multiqc_files.mix(FASTQC_FASTP.out.trim_json.collect{it[1]}.ifEmpty([])),
+        ch_multiqc_files = ch_multiqc_files.mix(FASTQC_FASTP.out.fastqc_raw_zip.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(FASTQC_FASTP.out.trim_json.collect{it[1]}.ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(contamination_stats.collect().ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(MIRNA_QUANT.out.mature_stats.collect({it[1]}).ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(MIRNA_QUANT.out.hairpin_stats.collect({it[1]}).ifEmpty([]))
@@ -239,13 +228,13 @@ workflow SMRNASEQ {
         ch_multiqc_files = ch_multiqc_files.mix(MIRNA_QUANT.out.mirtop_logs.collect().ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(MIRTRACE.out.results.collect().ifEmpty([]))
 
-    MULTIQC (
-        ch_multiqc_files.collect(),
-        ch_multiqc_config.toList(),
-        ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList()
-    )
-    multiqc_report = MULTIQC.out.report.toList()
+        MULTIQC (
+            ch_multiqc_files.collect(),
+            ch_multiqc_config.toList(),
+            ch_multiqc_custom_config.toList(),
+            ch_multiqc_logo.toList()
+        )
+        multiqc_report = MULTIQC.out.report.toList()
     }
 }
 

From e64be28c92d31cb5c5e75244caa62d785d6e0182 Mon Sep 17 00:00:00 2001
From: Rob Syme <rob.syme@gmail.com>
Date: Tue, 25 Apr 2023 05:36:16 +0000
Subject: [PATCH 27/32] Run mirtrace once for each adapter

---
 CHANGELOG.md                   |  2 ++
 modules/local/mirtrace.nf      | 16 +++++++---------
 subworkflows/local/mirtrace.nf |  3 ++-
 workflows/smrnaseq.nf          | 15 ++++++---------
 4 files changed, 17 insertions(+), 19 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 61f0e022..b5ff257a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,8 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+- Group samples by adapter sequence before running mirtrace.
+
 ## [v2.2.0](https://github.com/nf-core/smrnaseq/releases/tag/2.2.0) - 2023-04-25
 
 - [[#220](https://github.com/nf-core/smrnaseq/issues/220)] - Fixed an issue where miRTrace reports fastq basename instead of sample ID
diff --git a/modules/local/mirtrace.nf b/modules/local/mirtrace.nf
index 90dbd5f1..1815bf1b 100644
--- a/modules/local/mirtrace.nf
+++ b/modules/local/mirtrace.nf
@@ -7,7 +7,7 @@ process MIRTRACE_RUN {
         'quay.io/biocontainers/mirtrace:1.0.1--hdfd78af_1' }"
 
     input:
-    tuple val(meta), path(reads)
+    tuple val(adapter), val(ids), path(reads)
 
     output:
     path "mirtrace/*"  , emit: mirtrace
@@ -18,22 +18,20 @@ process MIRTRACE_RUN {
 
     script:
     // mirtrace protocol defaults to 'params.protocol' if not set
-    def primer = meta.adapter ? "--adapter ${meta.adapter}" : ""
+    def primer = adapter ? "--adapter ${adapter}" : ""
     def protocol = params.protocol == 'custom' ? '' : "--protocol $params.protocol"
     def java_mem = ''
-    def prefix = "${meta.id}"
     if(task.memory){
         tmem = task.memory.toBytes()
         java_mem = "-Xms${tmem} -Xmx${tmem}"
     }
+    def config_lines = [ids,reads]
+    .transpose()
+    .collect({ id, path -> "echo '${path},${id}' >> mirtrace_config" })
     """
     export mirtracejar=\$(dirname \$(which mirtrace))
-    for i in $reads
-    do
-        path=\$(realpath \${i})
-        prefix=$prefix
-        echo \$path","\$prefix
-    done > mirtrace_config
+    
+    ${config_lines.join("\n    ")}
 
     java $java_mem -jar \$mirtracejar/mirtrace.jar --mirtrace-wrapper-name mirtrace qc  \\
         --species $params.mirtrace_species \\
diff --git a/subworkflows/local/mirtrace.nf b/subworkflows/local/mirtrace.nf
index 38d51975..566b7a1b 100644
--- a/subworkflows/local/mirtrace.nf
+++ b/subworkflows/local/mirtrace.nf
@@ -6,10 +6,11 @@ include { MIRTRACE_RUN } from '../../modules/local/mirtrace'
 
 workflow MIRTRACE {
     take:
-    reads      // channel: [ val(meta), [ reads ] ]
+    reads      // channel: [ val(adapterseq), [ val(ids) ], [ path(reads) ] ]
 
     main:
     reads
+    | map { adapterseq, ids, read_collection -> [adapterseq, ids, read_collection*.first()]}
     | MIRTRACE_RUN
 
     emit:
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
index c3aaa55f..5b46b3db 100644
--- a/workflows/smrnaseq.nf
+++ b/workflows/smrnaseq.nf
@@ -139,11 +139,10 @@ workflow SMRNASEQ {
     //
     FASTQC_FASTP.out.adapterseq
     .join( ch_cat_fastq )
-    .map { meta, adapterseq, fastq -> [meta + [adapter:adapterseq], fastq] }
-    .collect()
+    .map { meta, adapterseq, fastq -> [adapterseq, meta.id, fastq] }
+    .groupTuple()
     .set { ch_mitrace_inputs }
 
-
     MIRTRACE(ch_mitrace_inputs)
     ch_versions = ch_versions.mix(MIRTRACE.out.versions.ifEmpty(null))
 
@@ -173,7 +172,7 @@ workflow SMRNASEQ {
         reference_mature,
         reference_hairpin,
         mirna_gtf,
-        CONTAMINANT_FILTER.out.filtered_reads
+        contamination_stats
     )
     ch_versions = ch_versions.mix(MIRNA_QUANT.out.versions.ifEmpty(null))
 
@@ -182,10 +181,8 @@ workflow SMRNASEQ {
     //
     genome_stats = Channel.empty()
     if (params.fasta){
-        ch_fasta = file(params.fasta)
-        GENOME_QUANT ( ch_fasta, params.bowtie_index, MIRNA_QUANT.out.unmapped )
-        GENOME_QUANT.out.stats
-            .set { genome_stats }
+        GENOME_QUANT ( file(params.fasta), params.bowtie_index, MIRNA_QUANT.out.unmapped )
+        genome_stats = GENOME_QUANT.out.stats
         ch_versions = ch_versions.mix(GENOME_QUANT.out.versions)
 
         if (!params.skip_mirdeep) {
@@ -222,9 +219,9 @@ workflow SMRNASEQ {
         ch_multiqc_files = ch_multiqc_files.mix(FASTQC_FASTP.out.fastqc_raw_zip.collect{it[1]}.ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(FASTQC_FASTP.out.trim_json.collect{it[1]}.ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(contamination_stats.collect().ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(genome_stats.collect({it[1]}).ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(MIRNA_QUANT.out.mature_stats.collect({it[1]}).ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(MIRNA_QUANT.out.hairpin_stats.collect({it[1]}).ifEmpty([]))
-        ch_multiqc_files = ch_multiqc_files.mix(genome_stats.collect({it[1]}).ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(MIRNA_QUANT.out.mirtop_logs.collect().ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(MIRTRACE.out.results.collect().ifEmpty([]))
 

From f6e87e4c11fe1a0d8e6353aa29cad2cbe842d915 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 25 Apr 2023 10:53:56 +0100
Subject: [PATCH 28/32] Update CHANGELOG.md

---
 CHANGELOG.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b5ff257a..83024af7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,8 +3,6 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-- Group samples by adapter sequence before running mirtrace.
-
 ## [v2.2.0](https://github.com/nf-core/smrnaseq/releases/tag/2.2.0) - 2023-04-25
 
 - [[#220](https://github.com/nf-core/smrnaseq/issues/220)] - Fixed an issue where miRTrace reports fastq basename instead of sample ID
@@ -13,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#205](https://github.com/nf-core/smrnaseq/issues/205)] - Fix mirTrace Report to be a single report again instead of per sample reports
 - [[#206](https://github.com/nf-core/smrnaseq/issues/206)] - Use % as separator in sed commands to enable conda working properly on OSX and Linux
 - [[#207](https://github.com/nf-core/smrnaseq/issues/224)] - Fix Samplesheet print error
+- Group samples by adapter sequence before running mirtrace
 
 ## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-20 Maroon Tin Dalmatian
 

From b405f204e93b9c71bd24d52add5827539cfdc23e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 25 Apr 2023 10:54:42 +0100
Subject: [PATCH 29/32] Update mirtrace.nf

---
 modules/local/mirtrace.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/mirtrace.nf b/modules/local/mirtrace.nf
index 1815bf1b..f37a4b3c 100644
--- a/modules/local/mirtrace.nf
+++ b/modules/local/mirtrace.nf
@@ -30,7 +30,7 @@ process MIRTRACE_RUN {
     .collect({ id, path -> "echo '${path},${id}' >> mirtrace_config" })
     """
     export mirtracejar=\$(dirname \$(which mirtrace))
-    
+
     ${config_lines.join("\n    ")}
 
     java $java_mem -jar \$mirtracejar/mirtrace.jar --mirtrace-wrapper-name mirtrace qc  \\

From 6f85f8f78500b4a4df4153589c27ba79e315a3aa Mon Sep 17 00:00:00 2001
From: Rob Syme <rob.syme@gmail.com>
Date: Wed, 26 Apr 2023 01:56:28 +0000
Subject: [PATCH 30/32] Ensure that users can skip fastp without breaking the
 workflow.

Also move fastqc_fastp.nf to local subworkflow as it's no longer
available in nf-core.
---
 subworkflows/{nf-core => local}/fastqc_fastp.nf | 4 ++--
 workflows/smrnaseq.nf                           | 3 +--
 2 files changed, 3 insertions(+), 4 deletions(-)
 rename subworkflows/{nf-core => local}/fastqc_fastp.nf (97%)

diff --git a/subworkflows/nf-core/fastqc_fastp.nf b/subworkflows/local/fastqc_fastp.nf
similarity index 97%
rename from subworkflows/nf-core/fastqc_fastp.nf
rename to subworkflows/local/fastqc_fastp.nf
index 5eb2b545..3ab260a8 100644
--- a/subworkflows/nf-core/fastqc_fastp.nf
+++ b/subworkflows/local/fastqc_fastp.nf
@@ -35,10 +35,10 @@ workflow FASTQC_FASTP {
 
     main:
 
-    ch_versions = Channel.empty()
-
+    ch_versions     = Channel.empty()
     fastqc_raw_html = Channel.empty()
     fastqc_raw_zip  = Channel.empty()
+    adapterseq      = reads.map { meta, _ -> [meta, null] }
     if (!params.skip_fastqc) {
         FASTQC_RAW (
             reads
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
index 5b46b3db..0f8b16a7 100644
--- a/workflows/smrnaseq.nf
+++ b/workflows/smrnaseq.nf
@@ -59,7 +59,7 @@ if (!params.mirgenedb) {
 }
 
 include { INPUT_CHECK        } from '../subworkflows/local/input_check'
-include { FASTQC_FASTP       } from '../subworkflows/nf-core/fastqc_fastp'
+include { FASTQC_FASTP       } from '../subworkflows/local/fastqc_fastp'
 include { CONTAMINANT_FILTER } from '../subworkflows/local/contaminant_filter'
 include { MIRNA_QUANT        } from '../subworkflows/local/mirna_quant'
 include { GENOME_QUANT       } from '../subworkflows/local/genome_quant'
@@ -132,7 +132,6 @@ workflow SMRNASEQ {
         false
     )
     ch_versions = ch_versions.mix(FASTQC_FASTP.out.versions)
-    ch_reads = FASTQC_FASTP.out.reads
 
     //
     // SUBWORKFLOW: mirtrace QC

From 50b1ce88d86c23e4f7e6cd4a65a3a984d537b3ab Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Wed, 26 Apr 2023 10:29:59 +0200
Subject: [PATCH 31/32] Update CHANGELOG.md

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 83024af7..c115fd34 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#206](https://github.com/nf-core/smrnaseq/issues/206)] - Use % as separator in sed commands to enable conda working properly on OSX and Linux
 - [[#207](https://github.com/nf-core/smrnaseq/issues/224)] - Fix Samplesheet print error
 - Group samples by adapter sequence before running mirtrace
+- Remove `--skip_qc` parameter
 
 ## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-20 Maroon Tin Dalmatian
 

From 5c2b35491ef02c3d92aea743fcd9040ddeb6f48e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Wed, 26 Apr 2023 12:08:11 +0100
Subject: [PATCH 32/32] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c115fd34..fe86157a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [v2.2.0](https://github.com/nf-core/smrnaseq/releases/tag/2.2.0) - 2023-04-25
+## [v2.2.0](https://github.com/nf-core/smrnaseq/releases/tag/2.2.0) - 2023-04-26
 
 - [[#220](https://github.com/nf-core/smrnaseq/issues/220)] - Fixed an issue where miRTrace reports fastq basename instead of sample ID
 - [[#208](https://github.com/nf-core/smrnaseq/issues/208)] - Fixed usability of `--skip_qc` parameter