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nf-core · Aug 26, 2024 · 4a73a71 · 4a73a71
2 parents 46ed8de + ae06cf8
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -36,6 +36,7 @@ jobs:
           - "test_index"
           - "test_technical_repeats"
           - "test_mirgenedb"
+          - "test_skipfastp"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,19 +5,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v2.4.0dev - 2024-XX-XX - X
 
-- [[#349]](https://github.com/nf-core/smrnaseq/pull/349) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347), change conda-base to conda-forge channel
+- [[#349]](https://github.com/nf-core/smrnaseq/pull/349) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347), change conda-base to conda-forge channel.
 - [[#350]](https://github.com/nf-core/smrnaseq/pull/350) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347), set python version to 3.7 to fix pysam issue.
-- [[#361]](https://github.com/nf-core/smrnaseq/pull/361) by [[#332]](https://github.com/nf-core/smrnaseq/issues/332) - Fix documentation to use only single-end.
+- [[#361]](https://github.com/nf-core/smrnaseq/pull/361) - Fix [[#332]](https://github.com/nf-core/smrnaseq/issues/332) - Fix documentation to use only single-end.
 - [[#364]](https://github.com/nf-core/smrnaseq/pull/364) - Fix [Protocol inheritance issue](https://github.com/nf-core/smrnaseq/issues/351) - fixing protocol inheritance from subworkflow with move to config profile(s) for different protocols.
 - [[#372]](https://github.com/nf-core/smrnaseq/pull/372) - Fix [Plain test profile](https://github.com/nf-core/smrnaseq/issues/371) - Updated default protocol value to "custom".
 - [[#374]](https://github.com/nf-core/smrnaseq/pull/374) - Fix [default tests](https://github.com/nf-core/smrnaseq/issues/375) so that they do not require additional profiles in CI. Change GitHub CI fail-fast strategy to false.
-- [[#375]](https://github.com/nf-core/smrnaseq/pull/375) - Test merging of [technical repeats](https://github.com/nf-core/smrnaseq/issues/212).
+- [[#375]](https://github.com/nf-core/smrnaseq/pull/375) - Test [technical repeats](https://github.com/nf-core/smrnaseq/issues/212) - Test merging of technical repeats.
 - [[#377]](https://github.com/nf-core/smrnaseq/pull/377) - Fix [Linting](https://github.com/nf-core/smrnaseq/issues/369) - Fixed linting warnings and updated modules & subworkflows.
 - [[#378]](https://github.com/nf-core/smrnaseq/pull/378) - Fix [`--mirtrace_species` bug](<(https://github.com/nf-core/smrnaseq/issues/348)>). Make `MIRTRACE` process conditional. Add mirgenedb test.
-- [[#380]](https://github.com/nf-core/smrnaseq/pull/380) - Fix checking number of samples which causes error in plotMDS. Add nf-tests for local modules using custom R scripts: [edgeR_mirBase.R](https://github.com/nf-core/smrnaseq/issues/187).
-- [[#381]](https://github.com/nf-core/smrnaseq/pull/381) - Update CI tests to nf-tests [Convert tests to nf-tests](https://github.com/nf-core/smrnaseq/issues/379).
-- [[#382]](https://github.com/nf-core/smrnaseq/pull/382) - Add nf-tests for local modules using custom R scripts: [collapse_mirtop.R](https://github.com/nf-core/smrnaseq/issues/174).
-- [[#384]](https://github.com/nf-core/smrnaseq/pull/384) - Fix filter stats module and add filter contaminants test profile: [filter status bug fix](https://github.com/nf-core/smrnaseq/issues/360).
+- [[#380]](https://github.com/nf-core/smrnaseq/pull/380) - Fix [edgeR_mirBase.R](https://github.com/nf-core/smrnaseq/issues/187) - Fix checking number of samples which causes error in plotMDS. Add nf-tests for local modules using custom R scripts.
+- [[#381]](https://github.com/nf-core/smrnaseq/pull/381) - Update [Convert tests to nf-tests](https://github.com/nf-core/smrnaseq/issues/379) - CI tests to nf-tests.
+- [[#382]](https://github.com/nf-core/smrnaseq/pull/382) - Add [collapse_mirtop.R](https://github.com/nf-core/smrnaseq/issues/174) - Add nf-tests for local modules using custom R scripts.
+- [[#383]](https://github.com/nf-core/smrnaseq/pull/383) - Fix [parameter `--skip_fastp` throws an error](https://github.com/nf-core/smrnaseq/issues/263) - Fix parameter --skip_fastp.
+- [[#384]](https://github.com/nf-core/smrnaseq/pull/384) - Fix [filter status bug fix](https://github.com/nf-core/smrnaseq/issues/360) - Fix filter stats module and add filter contaminants test profile.
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -70,6 +70,12 @@ process {
                 mode: params.publish_dir_mode,
                 pattern: "*.fail.fastq.gz",
                 enabled: params.save_trimmed_fail
+            ],
+            [
+                path: { "${params.outdir}/fastp/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastp.fastq.gz",
+                enabled: params.save_merged
             ]
         ]
     }

diff --git a/conf/test_skipfastp.config b/conf/test_skipfastp.config
@@ -0,0 +1,35 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/smrnaseq -profile test_skipfastp,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function skipping trimming'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+
+    input            = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet_skipfastp.csv'
+
+    mirtrace_species         = 'hsa'
+    skip_mirdeep             = true
+    skip_fastp               = true
+    save_merged              = false
+    save_aligned_mirna_quant = false
+
+    cleanup                  = true //Otherwise tests dont run through properly.
+}
+
+// Do not include any additional config so it defaults to protocol custom
diff --git a/nextflow.config b/nextflow.config
@@ -239,6 +239,7 @@ profiles {
 
     }
 
+
     test                           { includeConfig 'conf/test.config' }
     test_umi                       { includeConfig 'conf/test_umi.config' }
     test_no_genome                 { includeConfig 'conf/test_no_genome.config' }
@@ -247,7 +248,7 @@ profiles {
     test_index                     { includeConfig 'conf/test_index.config' }
     test_technical_repeats         { includeConfig 'conf/test_technical_repeats.config' }
     test_mirgenedb                 { includeConfig 'conf/test_mirgenedb.config' }
-
+    test_skipfastp              { includeConfig 'conf/test_skipfastp.config' }
 
 
     //Protocol specific profiles

diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
@@ -160,12 +160,23 @@ workflow NFCORE_SMRNASEQ {
     //
     // MODULE: mirtrace QC
     //
-    FASTQ_FASTQC_UMITOOLS_FASTP.out.adapter_seq
-    .join( ch_reads_for_mirna )
-    .dump()
-    .map { meta, adapter_seq, reads -> [adapter_seq, meta.id, reads] }
-    .groupTuple()
-    .set { ch_mirtrace_inputs }
+
+    // Define the main adapter sequence channel
+    ch_adapter_seq = FASTQ_FASTQC_UMITOOLS_FASTP.out.adapter_seq
+
+    // Define a fallback channel with the default value "custom"
+    ch_fallback_adapter_seq = ch_reads_for_mirna.map { meta, reads -> [meta, 'custom'] }
+
+    // Change to fallback channel if ch_adapter_seq is empty
+    ch_adapter_seq = ch_adapter_seq ? ch_fallback_adapter_seq : ch_adapter_seq
+
+    // Now join the adapter sequence channel with the reads channel
+    ch_adapter_seq
+        .join(ch_reads_for_mirna)
+        .map { meta, adapter_seq, reads -> [adapter_seq, meta.id, reads] }
+        .groupTuple()
+        .map { adapter_seq, ids, reads_list -> [adapter_seq, ids, reads_list.flatten()] }
+        .set { ch_mirtrace_inputs }
 
     //
     // SUBWORKFLOW: MIRTRACE