From 262672cbfcdc22aac5b067d1d53d4a18b746b0e4 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 13 Sep 2024 16:47:38 +0100 Subject: [PATCH 1/5] slight fixes for rnaseq prepro --- .../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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 4c7b25f8e..14da422eb 100644 --- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf +++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf @@ -181,7 +181,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.versions) ch_multiqc_files = FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_raw_zip .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_zip) - .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json.map{tuple(it[0], [it[1]])}) + .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json) .mix(ch_multiqc_files) } @@ -209,6 +209,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { ch_multiqc_files = ch_multiqc_files .mix( ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv') + .map { [[], it] } ) // From 3701544623b6de1a56cc27a44466b749bb7417bf Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 13 Sep 2024 16:57:47 +0000 Subject: [PATCH 2/5] Remove chunk duplicated from subworkflow --- workflows/rnaseq/main.nf | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index 0b702e641..2ee8384f4 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -167,25 +167,6 @@ workflow RNASEQ { meta, num_reads -> return [ meta.id, num_reads > params.min_trimmed_reads.toFloat() ] } - // - // Get list of samples that failed trimming threshold for MultiQC report - // - ch_trim_read_count - .map { - meta, num_reads -> - if (num_reads <= params.min_trimmed_reads.toFloat()) { - return [ "$meta.id\t$num_reads" ] - } - } - .collect() - .map { - tsv_data -> - def header = ["Sample", "Reads after trimming"] - sample_status_header_multiqc.text + multiqcTsvFromList(tsv_data, header) - } - .set { ch_fail_trimming_multiqc } - - ch_multiqc_files = ch_multiqc_files.mix(ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv')) // // SUBWORKFLOW: Alignment with STAR and gene/transcript quantification with Salmon From 5c6982c145699dd1651cf06d3f2140ac5755d8a5 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 13 Sep 2024 17:00:28 +0000 Subject: [PATCH 3/5] Try from branch --- modules.json | 4 ++-- .../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules.json b/modules.json index fc53bd567..bb42dadd3 100644 --- a/modules.json +++ b/modules.json @@ -324,8 +324,8 @@ "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_qc_trim_filter_setstrandedness": { - "branch": "master", - "git_sha": "8c47be6a114b82a6e6d2f5320b3b5c67579956c0", + "branch": "fastq_prepro_trimfail_fix", + "git_sha": "5ccbeafc08c38098a5eae0583f97ea56518278ab", "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 14da422eb..4ed073efc 100644 --- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf +++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf @@ -209,7 +209,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { ch_multiqc_files = ch_multiqc_files .mix( ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv') - .map { [[], it] } + .map { [[:], it] } ) // From 3e9af61bd3fb9f931c5a7058cb17be5240fdfb6f Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 16 Sep 2024 12:35:22 +0100 Subject: [PATCH 4/5] install subworkflow from master --- modules.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules.json b/modules.json index df4c6d69d..30090ab26 100644 --- a/modules.json +++ b/modules.json @@ -324,8 +324,8 @@ "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_qc_trim_filter_setstrandedness": { - "branch": "fastq_prepro_trimfail_fix", - "git_sha": "5ccbeafc08c38098a5eae0583f97ea56518278ab", + "branch": "master", + "git_sha": "ee3b8b84da02320fff5f3f2dc1d6f9b72d7cd5af", "installed_by": ["subworkflows"] }, "fastq_subsample_fq_salmon": { From 5703690c59aab36988374c045e07adbd6da42754 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 16 Sep 2024 12:41:15 +0100 Subject: [PATCH 5/5] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f35bf876c..9ba7510ff 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ Special thanks to the following for their contributions to the release: - [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev - [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names - [PR #1381](https://github.com/nf-core/rnaseq/pull/1381) - Update all modules following massive conda usage update in nf-core modules +- [PR #1382](https://github.com/nf-core/rnaseq/pull/1381) - Slight fixes for rnaseq preprocessing ## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04