From 42d80faa153d6000c58ae16874733388632d5ed3 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 19 Jul 2024 14:13:14 +0100 Subject: [PATCH 1/5] Fix the new call to preprocessing subworkflow --- workflows/rnaseq/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index 896159378..88fcd78fb 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -139,7 +139,7 @@ workflow RNASEQ { params.skip_fastqc || params.skip_qc, params.skip_trimming, params.skip_umi_extract, - !params.salmon_index && params.pseudo_aligner == 'salmon' && !skip_pseudo_alignment, + !params.salmon_index && params.pseudo_aligner == 'salmon' && !params.skip_pseudo_alignment, !params.sortmerna_index && params.remove_ribo_rna, params.trimmer, params.min_trimmed_reads, @@ -169,6 +169,7 @@ workflow RNASEQ { is_aws_igenome = true } } + print(is_aws_igenome) ALIGN_STAR ( ch_strand_inferred_filtered_fastq, From b8160d43f5cb1664ff5c8ca0a29b97fc8123ea97 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 19 Jul 2024 14:13:14 +0100 Subject: [PATCH 2/5] Fix the new call to preprocessing subworkflow --- workflows/rnaseq/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index 896159378..88fcd78fb 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -139,7 +139,7 @@ workflow RNASEQ { params.skip_fastqc || params.skip_qc, params.skip_trimming, params.skip_umi_extract, - !params.salmon_index && params.pseudo_aligner == 'salmon' && !skip_pseudo_alignment, + !params.salmon_index && params.pseudo_aligner == 'salmon' && !params.skip_pseudo_alignment, !params.sortmerna_index && params.remove_ribo_rna, params.trimmer, params.min_trimmed_reads, @@ -169,6 +169,7 @@ workflow RNASEQ { is_aws_igenome = true } } + print(is_aws_igenome) ALIGN_STAR ( ch_strand_inferred_filtered_fastq, From 3e293a8bddb4cb483196c76e5cce4e9244b17c51 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 19 Jul 2024 16:02:14 +0100 Subject: [PATCH 3/5] Fix the new call to preprocessing subworkflow --- modules.json | 2 +- .../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules.json b/modules.json index 8d89cfcbb..f197e3f65 100644 --- a/modules.json +++ b/modules.json @@ -324,7 +324,7 @@ }, "fastq_qc_trim_filter_setstrandedness": { "branch": "master", - "git_sha": "b86de50ab60c19ab40e70a4501820f4cb307050b", + "git_sha": "22c8d535286728605ccd229e5d1bb014cb965f8f", "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 cd69166f3..db73488f1 100644 --- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf +++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf @@ -134,7 +134,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { .mix(ch_fastq.single) .set { ch_filtered_reads } - ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) // // SUBWORKFLOW: Read QC, extract UMI and trim adapters with TrimGalore! From 6c8aa0bba8edb2c9b8a9446401ca9ec146101e32 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 19 Jul 2024 16:03:41 +0100 Subject: [PATCH 4/5] Remove print --- workflows/rnaseq/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index 88fcd78fb..7bf5d36e0 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -169,7 +169,6 @@ workflow RNASEQ { is_aws_igenome = true } } - print(is_aws_igenome) ALIGN_STAR ( ch_strand_inferred_filtered_fastq, From 4ed0cc6768e680c360081fbe23a7fc508b9b9ba1 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 19 Jul 2024 16:11:53 +0100 Subject: [PATCH 5/5] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ac293d86a..e62628fc6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -105,6 +105,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1340](https://github.com/nf-core/rnaseq/pull/1340) - Remove out-of-date Azure specific guidance - [PR #1341](https://github.com/nf-core/rnaseq/pull/1341) - Add rename in the MultiQC report for samples without techreps - [PR #1342](https://github.com/nf-core/rnaseq/pull/1342) - Factor out preprocessing +- [PR #1345](https://github.com/nf-core/rnaseq/pull/1345) - Fix preprocessing call ### Parameters