From ec1f25b9678f0ad0971784ea873e1da10a1fcf1f Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 16 Sep 2024 13:32:08 +0000
Subject: [PATCH 1/8] add nf-core pigz uncompress

---
 conf/modules.config                           |  5 ++
 modules.json                                  |  5 ++
 modules/nf-core/pigz/uncompress/main.nf       | 48 +++++++++++++++++++
 modules/nf-core/pigz/uncompress/meta.yml      | 42 ++++++++++++++++
 .../pigz/uncompress/tests/main.nf.test        | 33 +++++++++++++
 .../pigz/uncompress/tests/main.nf.test.snap   | 35 ++++++++++++++
 .../nf-core/pigz/uncompress/tests/tags.yml    |  2 +
 subworkflows/local/mirdeep2.nf                |  7 +--
 8 files changed, 174 insertions(+), 3 deletions(-)
 create mode 100644 modules/nf-core/pigz/uncompress/main.nf
 create mode 100644 modules/nf-core/pigz/uncompress/meta.yml
 create mode 100644 modules/nf-core/pigz/uncompress/tests/main.nf.test
 create mode 100644 modules/nf-core/pigz/uncompress/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/pigz/uncompress/tests/tags.yml

diff --git a/conf/modules.config b/conf/modules.config
index f1992ea2..37a55c1a 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -383,6 +383,11 @@ process {
     //
     // MIRDEEP
     //
+
+    withName: 'PIGZ_UNCOMPRESS' {
+        tag = {"${meta.id}"}
+    }
+
     withName: 'NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_MAPPER' {
         publishDir = [
             path: { "${params.outdir}/mirdeep2/mapper" },
diff --git a/modules.json b/modules.json
index 5d7f9eeb..dd1c1a5e 100644
--- a/modules.json
+++ b/modules.json
@@ -45,6 +45,11 @@
                         "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
                         "installed_by": ["modules"]
                     },
+                    "pigz/uncompress": {
+                        "branch": "master",
+                        "git_sha": "c00055a0b13d622b4f1f51a8e5be31deaf99ded7",
+                        "installed_by": ["modules"]
+                    },
                     "samtools/flagstat": {
                         "branch": "master",
                         "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
diff --git a/modules/nf-core/pigz/uncompress/main.nf b/modules/nf-core/pigz/uncompress/main.nf
new file mode 100644
index 00000000..11e43dff
--- /dev/null
+++ b/modules/nf-core/pigz/uncompress/main.nf
@@ -0,0 +1,48 @@
+process PIGZ_UNCOMPRESS {
+    label 'process_low'
+    //stageInMode 'copy' // this directive can be set in case the original input should be kept
+
+    conda "conda-forge::pigz"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pigz:2.8':
+        'biocontainers/pigz:2.8' }"
+
+    input:
+    tuple val(meta), path(zip)
+
+    output:
+    tuple val(meta), path("${uncompressed_filename}") , emit: file
+    path "versions.yml"                               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    uncompressed_filename = zip.toString() - '.gz'
+    // calling pigz -f to make it follow symlinks
+    """
+    unpigz \\
+        -p $task.cpus \\
+        -fk \\
+        $args \\
+        ${zip}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    uncompressed_filename = zip.toString() - '.gz'
+    """
+    touch ${zip.dropRight(3)}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\w*//' ))
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/pigz/uncompress/meta.yml b/modules/nf-core/pigz/uncompress/meta.yml
new file mode 100644
index 00000000..c2d16cd4
--- /dev/null
+++ b/modules/nf-core/pigz/uncompress/meta.yml
@@ -0,0 +1,42 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "pigz_uncompress"
+description: write your description here
+keywords:
+  - uncompress
+  - gzip
+  - parallelized
+tools:
+  - "pigz":
+      description: "Parallel implementation of the gzip algorithm."
+      homepage: "https://zlib.net/pigz/"
+      documentation: "https://zlib.net/pigz/pigz.pdf"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test']`
+  - zip:
+      type: file
+      description: Gzipped file
+      pattern: "*.{gzip}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test']`
+  - file:
+      type: file
+      description: File to compress
+      pattern: "*"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@lrauschning"
diff --git a/modules/nf-core/pigz/uncompress/tests/main.nf.test b/modules/nf-core/pigz/uncompress/tests/main.nf.test
new file mode 100644
index 00000000..62ab27e2
--- /dev/null
+++ b/modules/nf-core/pigz/uncompress/tests/main.nf.test
@@ -0,0 +1,33 @@
+nextflow_process {
+
+    name "Test Process PIGZ_UNCOMPRESS"
+    script "modules/nf-core/pigz/uncompress/main.nf"
+    process "PIGZ_UNCOMPRESS"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pigz"
+    tag "pigz/uncompress"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [ [ id:'test'],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                            ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/pigz/uncompress/tests/main.nf.test.snap b/modules/nf-core/pigz/uncompress/tests/main.nf.test.snap
new file mode 100644
index 00000000..126dd7d6
--- /dev/null
+++ b/modules/nf-core/pigz/uncompress/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a2d5ce72baa8b303f25afb9cf094f683"
+                ],
+                "file": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a2d5ce72baa8b303f25afb9cf094f683"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.03.0"
+        },
+        "timestamp": "2024-05-15T16:43:21.55056643"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/pigz/uncompress/tests/tags.yml b/modules/nf-core/pigz/uncompress/tests/tags.yml
new file mode 100644
index 00000000..6719a90a
--- /dev/null
+++ b/modules/nf-core/pigz/uncompress/tests/tags.yml
@@ -0,0 +1,2 @@
+pigz/uncompress:
+  - modules/nf-core/pigz/uncompress/**
diff --git a/subworkflows/local/mirdeep2.nf b/subworkflows/local/mirdeep2.nf
index 76afa8a4..f83415a5 100644
--- a/subworkflows/local/mirdeep2.nf
+++ b/subworkflows/local/mirdeep2.nf
@@ -3,6 +3,7 @@
 //
 
 include { MIRDEEP2_PIGZ   } from '../../modules/local/mirdeep2_prepare'
+include { PIGZ_UNCOMPRESS } from '../../modules/nf-core/pigz/uncompress/main'
 include { MIRDEEP2_MAPPER } from '../../modules/local/mirdeep2_mapper'
 include { MIRDEEP2_RUN    } from '../../modules/local/mirdeep2_run'
 
@@ -17,10 +18,10 @@ workflow MIRDEEP2 {
     main:
     ch_versions = Channel.empty()
 
-    MIRDEEP2_PIGZ ( reads )
-    ch_versions = ch_versions.mix(MIRDEEP2_PIGZ.out.versions.first())
+    PIGZ_UNCOMPRESS ( reads )
+    ch_versions = ch_versions.mix(PIGZ_UNCOMPRESS.out.versions.first())
 
-    MIRDEEP2_MAPPER ( MIRDEEP2_PIGZ.out.reads, index )
+    MIRDEEP2_MAPPER ( PIGZ_UNCOMPRESS.out.file, index )
     ch_versions = ch_versions.mix(MIRDEEP2_MAPPER.out.versions.first())
 
     MIRDEEP2_RUN ( fasta.map{meta,file->file}, MIRDEEP2_MAPPER.out.mirdeep2_inputs, hairpin, mature )

From c2b82b87ab13d427e82736d1846e4a1093815eb1 Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 16 Sep 2024 13:32:17 +0000
Subject: [PATCH 2/8] update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 44a03835..45c238e9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,6 +29,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#405]](https://github.com/nf-core/smrnaseq/pull/405) - Fix [Umicollapse algo wrong set](https://github.com/nf-core/smrnaseq/issues/404) - Fix potential bug in Umicollapse (not effective as we do not allow PE data in smrnaseq - but for consistency)
 - [[#420]](https://github.com/nf-core/smrnaseq/pull/420) - Fix [mirTrace produces an error in test nextflex](https://github.com/nf-core/smrnaseq/issues/419) - Allow config mode to be used in mirtrace/qc
 - [[#425]](https://github.com/nf-core/smrnaseq/pull/425) - Raise [minimum required NXF version for pipeline](https://github.com/nf-core/smrnaseq/issues/424) - usage of `arity` in some modules now requires this
+- [[#426]](https://github.com/nf-core/smrnaseq/pull/426) - Add [nf-core mirtop](https://github.com/nf-core/smrnaseq/issues/417) - replace local `mirtop`
+- [[#427]](https://github.com/nf-core/smrnaseq/pull/427) - Add [nf-core pigz uncompress](https://github.com/nf-core/smrnaseq/issues/422) - replace local `mirdeep_pigz`
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch
 

From 6090c0fb810976516150b811a23a859dd526dafa Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 16 Sep 2024 15:18:09 +0000
Subject: [PATCH 3/8] copy staged files

---
 conf/modules.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/modules.config b/conf/modules.config
index 37a55c1a..cad31ce3 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -386,6 +386,7 @@ process {
 
     withName: 'PIGZ_UNCOMPRESS' {
         tag = {"${meta.id}"}
+        stageInMode = 'copy'
     }
 
     withName: 'NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_MAPPER' {

From 41b5cbfd37a8023cee6973a65a69074d7ecf1e6d Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 16 Sep 2024 15:18:20 +0000
Subject: [PATCH 4/8] remove unused local module

---
 modules/local/mirdeep2_prepare.nf | 31 -------------------------------
 subworkflows/local/mirdeep2.nf    |  1 -
 2 files changed, 32 deletions(-)
 delete mode 100644 modules/local/mirdeep2_prepare.nf

diff --git a/modules/local/mirdeep2_prepare.nf b/modules/local/mirdeep2_prepare.nf
deleted file mode 100644
index ce66b9f1..00000000
--- a/modules/local/mirdeep2_prepare.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-process MIRDEEP2_PIGZ {
-    label 'process_low'
-    tag "$meta.id"
-
-    // TODO maybe create a mulled container and uncompress within mirdeep2_mapper?
-    conda 'bioconda::bioconvert=1.1.1'
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconvert:1.1.1--pyhdfd78af_0' :
-        'biocontainers/bioconvert:1.1.1--pyhdfd78af_0' }"
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path("*.{fastq,fq}"), emit: reads
-    path "versions.yml"                  , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    """
-    pigz -f -d -p $task.cpus $reads
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
-    END_VERSIONS
-    """
-
-}
diff --git a/subworkflows/local/mirdeep2.nf b/subworkflows/local/mirdeep2.nf
index f83415a5..40dd9f29 100644
--- a/subworkflows/local/mirdeep2.nf
+++ b/subworkflows/local/mirdeep2.nf
@@ -2,7 +2,6 @@
 // Quantify mirna with bowtie and mirtop
 //
 
-include { MIRDEEP2_PIGZ   } from '../../modules/local/mirdeep2_prepare'
 include { PIGZ_UNCOMPRESS } from '../../modules/nf-core/pigz/uncompress/main'
 include { MIRDEEP2_MAPPER } from '../../modules/local/mirdeep2_mapper'
 include { MIRDEEP2_RUN    } from '../../modules/local/mirdeep2_run'

From b54447f235120eea13afeb9df48204659ca07ed9 Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 16 Sep 2024 15:23:03 +0000
Subject: [PATCH 5/8] remove unused local mirtop

---
 modules/local/mirtop_quant.nf | 43 -----------------------------------
 1 file changed, 43 deletions(-)
 delete mode 100644 modules/local/mirtop_quant.nf

diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf
deleted file mode 100644
index cdb6d32b..00000000
--- a/modules/local/mirtop_quant.nf
+++ /dev/null
@@ -1,43 +0,0 @@
-process MIRTOP_QUANT {
-    label 'process_medium'
-
-    conda 'mirtop=0.4.25 bioconda::samtools=1.20 conda-forge::r-base=4.1.1 conda-forge::r-data.table=1.14.2 python=3.7'
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' :
-        'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }"
-
-    input:
-    path ("bams/*")
-    path hairpin
-    path gtf
-    val mirtrace_species
-
-    output:
-    path "mirtop/mirtop.gff"        , emit: mirtop_gff
-    path "mirtop/mirtop.tsv"        , emit: mirtop_table
-    path "mirtop/mirtop_rawData.tsv", emit: mirtop_rawdata
-    path "mirtop/stats/*"           , emit: logs
-    path "versions.yml"             , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def filter_species = params.mirgenedb ? params.mirgenedb_species : mirtrace_species
-    """
-    #Cleanup the GTF if mirbase html form is broken
-    GTF="$gtf"
-    sed 's/&gt;/>/g' \$GTF | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' | sed -e :a -e '/^\\n*\$/{\$d;N;};/\\n\$/ba' > \${GTF}_html_cleaned.gtf
-    mirtop gff --hairpin $hairpin --gtf \${GTF}_html_cleaned.gtf -o mirtop --sps $filter_species ./bams/*
-    mirtop counts --hairpin $hairpin --gtf \${GTF}_html_cleaned.gtf -o mirtop --sps $filter_species --add-extra --gff mirtop/mirtop.gff
-    mirtop export --format isomir --hairpin $hairpin --gtf \${GTF}_html_cleaned.gtf --sps $filter_species -o mirtop mirtop/mirtop.gff
-    mirtop stats mirtop/mirtop.gff --out mirtop/stats
-    mv mirtop/stats/mirtop_stats.log mirtop/stats/full_mirtop_stats.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        mirtop: \$(echo \$(mirtop --version 2>&1) | sed 's/^.*mirtop //')
-    END_VERSIONS
-    """
-
-}

From 9a24f8dbd3c2a357418ddbbce1f8709fd0bcbf9e Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 16 Sep 2024 15:30:30 +0000
Subject: [PATCH 6/8] remove unused local mirtop quant

---
 conf/modules.config               | 9 +--------
 subworkflows/local/mirna_quant.nf | 1 -
 2 files changed, 1 insertion(+), 9 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 0452d94b..5dc3c678 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -329,14 +329,7 @@ process {
             enabled: params.save_aligned_mirna_quant
         ]
     }
-    withName: 'MIRTOP_QUANT' {
-        publishDir = [
-            //mirtop already part of the output folder
-            path: { "${params.outdir}/mirna_quant/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
+
 
     // Mirtop
 
diff --git a/subworkflows/local/mirna_quant.nf b/subworkflows/local/mirna_quant.nf
index e8a99a4c..cbca7956 100644
--- a/subworkflows/local/mirna_quant.nf
+++ b/subworkflows/local/mirna_quant.nf
@@ -19,7 +19,6 @@ include {   BAM_SORT_STATS_SAMTOOLS as BAM_STATS_MATURE
             BAM_SORT_STATS_SAMTOOLS as BAM_STATS_HAIRPIN   } from '../nf-core/bam_sort_stats_samtools'
 
 include { SEQCLUSTER_COLLAPSE  } from '../../modules/nf-core/seqcluster/collapse/main'
-include { MIRTOP_QUANT         } from '../../modules/local/mirtop_quant.nf'
 include { TABLE_MERGE          } from '../../modules/local/datatable_merge/datatable_merge.nf'
 include { EDGER_QC             } from '../../modules/local/edger_qc/edger_qc.nf'
 include { BAM_STATS_MIRNA_MIRTOP } from '../../subworkflows/nf-core/bam_stats_mirna_mirtop/main'

From 21b552222dc0a59a9eea8935fa74e88835684226 Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 17 Sep 2024 17:20:48 +0000
Subject: [PATCH 7/8] save intermediates in tests

---
 conf/test_contamination_tech_reps.config | 3 +--
 conf/test_mirgenedb.config               | 3 +--
 conf/test_skipfastp.config               | 3 +--
 conf/test_technical_repeats.config       | 3 +--
 conf/test_umi.config                     | 7 ++++---
 5 files changed, 8 insertions(+), 11 deletions(-)

diff --git a/conf/test_contamination_tech_reps.config b/conf/test_contamination_tech_reps.config
index ffcfafb6..f164bde4 100644
--- a/conf/test_contamination_tech_reps.config
+++ b/conf/test_contamination_tech_reps.config
@@ -24,8 +24,7 @@ params {
     input      = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet_technical_repeats_short.csv'
 
     mirtrace_species         = 'hsa'
-    save_merged              = false
-    save_aligned_mirna_quant = false
+    save_intermediates       = true
 
     skip_multiqc             = true
     skip_mirdeep             = true
diff --git a/conf/test_mirgenedb.config b/conf/test_mirgenedb.config
index 8bd1c46a..ea7babb4 100644
--- a/conf/test_mirgenedb.config
+++ b/conf/test_mirgenedb.config
@@ -31,8 +31,7 @@ params {
     mirgenedb_species        = "Hsa"
 
     skip_mirdeep             = true
-    save_merged              = false
-    save_aligned_mirna_quant = false
+    save_intermediates       = true
 
 }
 
diff --git a/conf/test_skipfastp.config b/conf/test_skipfastp.config
index 6ccd228d..82f2f2f8 100644
--- a/conf/test_skipfastp.config
+++ b/conf/test_skipfastp.config
@@ -29,8 +29,7 @@ params {
     mirtrace_species         = 'hsa'
     skip_mirdeep             = true
     skip_fastp               = true
-    save_merged              = false
-    save_aligned_mirna_quant = false
+    save_intermediates       = true
 }
 
 // Do not include any additional config so it defaults to protocol custom
diff --git a/conf/test_technical_repeats.config b/conf/test_technical_repeats.config
index b462a5ad..2c75e9bc 100644
--- a/conf/test_technical_repeats.config
+++ b/conf/test_technical_repeats.config
@@ -26,8 +26,7 @@ params {
 
     mirtrace_species         = 'hsa'
     skip_mirdeep             = true
-    save_merged              = false
-    save_aligned_mirna_quant = false
+    save_intermediates       = true
 
     skip_fastqc                 = true
     skip_multiqc                = true
diff --git a/conf/test_umi.config b/conf/test_umi.config
index 4cb1be2b..16bc7256 100644
--- a/conf/test_umi.config
+++ b/conf/test_umi.config
@@ -30,9 +30,10 @@ params {
 
     //UMI Specific testcase
     with_umi = true
-    umitools_extract_method = 'regex'
-    umitools_bc_pattern = '.+(?P<discard_1>AACTGTAGGCACCATCAAT){s<=2}(?P<umi_1>.{12})(?P<discard_2>.*)'
-    save_umi_intermeds = true
+    umitools_extract_method  = 'regex'
+    umitools_bc_pattern      = '.+(?P<discard_1>AACTGTAGGCACCATCAAT){s<=2}(?P<umi_1>.{12})(?P<discard_2>.*)'
+    save_umi_intermeds       = true
+    save_intermediates       = true
 }
 
 // Include illumina config to run test without additional profiles

From a41a338d0de09ecaf69c6905c70dda0c6b5154ed Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 17 Sep 2024 17:36:04 +0000
Subject: [PATCH 8/8] save intermediates

---
 conf/test_nextflex.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/test_nextflex.config b/conf/test_nextflex.config
index 6967c933..4db4a2d3 100644
--- a/conf/test_nextflex.config
+++ b/conf/test_nextflex.config
@@ -28,6 +28,7 @@ params {
     mirtrace_species    = 'hsa'
 
     skip_mirdeep             = true
+    save_intermediates       = true
 
 }