From 95b29277fe1dd8348941edf2314244282aa0e17c Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 15 Oct 2024 12:19:06 +0100 Subject: [PATCH 1/3] Fix ifEmpty() issues with trimming --- modules.json | 6 +++--- subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf | 2 +- .../nf-core/fastq_fastqc_umitools_trimgalore/main.nf | 2 +- .../tests/main.nf.test.snap | 4 ++-- .../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf | 4 ++-- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/modules.json b/modules.json index ffcdcaf40..736ec500a 100644 --- a/modules.json +++ b/modules.json @@ -327,17 +327,17 @@ }, "fastq_fastqc_umitools_fastp": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "4026bab16a91b1b0b18d80ff465819ca725f33fd", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_fastqc_umitools_trimgalore": { "branch": "master", - "git_sha": "53fcc37e256ea30818fb793bbe98b63e4a40deb8", + "git_sha": "4026bab16a91b1b0b18d80ff465819ca725f33fd", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_qc_trim_filter_setstrandedness": { "branch": "master", - "git_sha": "aef0e7467478130e861365232c3c4cc3247938ec", + "git_sha": "4026bab16a91b1b0b18d80ff465819ca725f33fd", "installed_by": ["subworkflows"] }, "fastq_subsample_fq_salmon": { diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf index ab6cbb320..9c355a5e3 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf +++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf @@ -160,5 +160,5 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP { fastqc_trim_html // channel: [ val(meta), [ html ] ] fastqc_trim_zip // channel: [ val(meta), [ zip ] ] - versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf index db2e5b329..4ffc36984 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf @@ -119,5 +119,5 @@ workflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE { trim_log // channel: [ val(meta), [ txt ] ] trim_read_count // channel: [ val(meta), val(count) ] - versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap index 264ffb222..46bf3acf2 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap @@ -377,7 +377,7 @@ ], [ - null + ] ], "meta": { @@ -521,4 +521,4 @@ }, "timestamp": "2024-07-22T17:06:09.844235" } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf index c655af415..05078d23d 100644 --- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf +++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf @@ -139,7 +139,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { // // SUBWORKFLOW: Read QC, extract UMI and trim adapters with TrimGalore! // - if (trimmer == 'trimgalore') { + if (trimmer == 'trimgalore' && !skip_trimming) { FASTQ_FASTQC_UMITOOLS_TRIMGALORE ( ch_filtered_reads, skip_fastqc, @@ -162,7 +162,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { // // SUBWORKFLOW: Read QC, extract UMI and trim adapters with fastp // - if (trimmer == 'fastp') { + if (trimmer == 'fastp' && !skip_trimming) { FASTQ_FASTQC_UMITOOLS_FASTP ( ch_filtered_reads, skip_fastqc, From f6355ee88cc3d2ce82dd9d31e6d64346a6e06dd3 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 15 Oct 2024 12:23:45 +0100 Subject: [PATCH 2/3] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 05a0bb006..3419ba5c6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ Special thanks to the following for their contributions to the release: - [PR #1401](https://github.com/nf-core/rnaseq/pull/1401) - Template update for nf-core/tools v3.0.1 - [PR #1405](https://github.com/nf-core/rnaseq/pull/1405) - Fix bad variable name in subworkflow - [PR #1406](https://github.com/nf-core/rnaseq/pull/1406) - Keep only one samplesheetToList +- [PR #1410](https://github.com/nf-core/rnaseq/pull/1410) - Fix issues caused by empty versions from trimming subworkflows ### Parameters From a391518419c81e8fc2cebf770cae6d6fc3786af5 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 15 Oct 2024 20:22:47 +0100 Subject: [PATCH 3/3] Update rnaseq prepro --- modules.json | 2 +- .../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules.json b/modules.json index 736ec500a..6a263bfc8 100644 --- a/modules.json +++ b/modules.json @@ -337,7 +337,7 @@ }, "fastq_qc_trim_filter_setstrandedness": { "branch": "master", - "git_sha": "4026bab16a91b1b0b18d80ff465819ca725f33fd", + "git_sha": "9082d6440bdffbb4f5d9bd9d753361933b3febcb", "installed_by": ["subworkflows"] }, "fastq_subsample_fq_salmon": { diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf index 05078d23d..c655af415 100644 --- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf +++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf @@ -139,7 +139,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { // // SUBWORKFLOW: Read QC, extract UMI and trim adapters with TrimGalore! // - if (trimmer == 'trimgalore' && !skip_trimming) { + if (trimmer == 'trimgalore') { FASTQ_FASTQC_UMITOOLS_TRIMGALORE ( ch_filtered_reads, skip_fastqc, @@ -162,7 +162,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { // // SUBWORKFLOW: Read QC, extract UMI and trim adapters with fastp // - if (trimmer == 'fastp' && !skip_trimming) { + if (trimmer == 'fastp') { FASTQ_FASTQC_UMITOOLS_FASTP ( ch_filtered_reads, skip_fastqc,