From 1b09cba8ebe918386a57ced9a37cdb9961ea9498 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 8 Oct 2024 14:59:55 +1300 Subject: [PATCH] Cleaned busco sample names and added files to multiqc --- assets/multiqc_config.yml | 6 ++++++ subworkflows/local/align_rnaseq.nf | 5 +++-- subworkflows/local/preprocess_rnaseq.nf | 9 ++++++--- workflows/genepal.nf | 10 ++++++++++ 4 files changed, 25 insertions(+), 5 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 4169abb..67df9ee 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -34,3 +34,9 @@ module_order: info: "Annotation completeness statistics" path_filters_exclude: - "*seqkit.rmdup.fasta.txt" + +extra_fn_clean_exts: + - ".seqkit" + - ".rmdup" + - type: regex + pattern: "^short_summary\\.specific\\..*_odb10\\." diff --git a/subworkflows/local/align_rnaseq.nf b/subworkflows/local/align_rnaseq.nf index 0ad3b59..71d4169 100644 --- a/subworkflows/local/align_rnaseq.nf +++ b/subworkflows/local/align_rnaseq.nf @@ -76,6 +76,7 @@ workflow ALIGN_RNASEQ { ch_versions = ch_versions.mix(SAMTOOLS_CAT.out.versions.first()) emit: - bam = ch_samtools_bam // channel: [ [ id: target_assembly, single_end ], [ bam ] ] - versions = ch_versions // channel: [ versions.yml ] + bam = ch_samtools_bam // channel: [ [ id: target_assembly, single_end ], [ bam ] ] + star_log_final = STAR_ALIGN.out.log_final // channel: [ [ id: sample.on.assembly, single_end ], log ] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/preprocess_rnaseq.nf b/subworkflows/local/preprocess_rnaseq.nf index b13a3c9..8f91158 100644 --- a/subworkflows/local/preprocess_rnaseq.nf +++ b/subworkflows/local/preprocess_rnaseq.nf @@ -117,7 +117,10 @@ workflow PREPROCESS_RNASEQ { emit: - trim_reads = ch_emitted_reads // channel: [ [ id, single_end ], [ fq ] ] - reads_target = ch_reads_target // channel: [ [ id, single_end ], assembly_id ] - versions = ch_versions // channel: [ versions.yml ] + trim_reads = ch_emitted_reads // channel: [ [ id, single_end ], [ fq ] ] + reads_target = ch_reads_target // channel: [ [ id, single_end ], assembly_id ] + fastqc_raw_zip = FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_raw_zip // channel: [ [ id, single_end ], zip ] + trim_json = FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json // channel: [ [ id, single_end ], json ] + fastqc_trim_zip = FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_zip // channel: [ [ id, single_end ], zip ] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/workflows/genepal.nf b/workflows/genepal.nf index 65e10e3..7cc3226 100644 --- a/workflows/genepal.nf +++ b/workflows/genepal.nf @@ -92,6 +92,12 @@ workflow GENEPAL { ch_trim_reads = PREPROCESS_RNASEQ.out.trim_reads ch_reads_target = PREPROCESS_RNASEQ.out.reads_target + + ch_multiqc_files = ch_multiqc_files + | mix(PREPROCESS_RNASEQ.out.fastqc_raw_zip) + | mix(PREPROCESS_RNASEQ.out.trim_json) + | mix(PREPROCESS_RNASEQ.out.fastqc_trim_zip) + ch_versions = ch_versions.mix(PREPROCESS_RNASEQ.out.versions) // SUBWORKFLOW: ALIGN_RNASEQ @@ -103,6 +109,10 @@ workflow GENEPAL { ) ch_rnaseq_bam = ALIGN_RNASEQ.out.bam + + ch_multiqc_files = ch_multiqc_files + | mix(ALIGN_RNASEQ.out.star_log_final) + ch_versions = ch_versions.mix(ALIGN_RNASEQ.out.versions) // MODULE: PREPARE_EXT_PROTS