From 3e4a92349386a1d61181126fc36ad092d641ec5b Mon Sep 17 00:00:00 2001 From: Austyn Trull Date: Wed, 4 Oct 2023 15:11:11 -0500 Subject: [PATCH] Reformatting the multiqc reports --- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- workflows/scnanoseq.nf | 24 ++++++++++++++++++++++-- 3 files changed, 25 insertions(+), 5 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 4306b66..2c87ce5 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -39,14 +39,14 @@ top_modules: info: "This section of the report shows FastQC results of the trimmed data" path_filters: - - "*filtered*fastqc*" + - "*trimmed*fastqc*" - fastqc: name: "FastQC (post extract)" anchor: "fastqc_postextract" info: "This section of the report shows FastQC results of the trimmed and umi extracted data" path_filters: - - "*umi_extract*fastqc*" + - "*extracted*fastqc*" section_comments: fastqc_posttrim: "Please note that if 'prowler' is selected as the trimming diff --git a/nextflow.config b/nextflow.config index db1d065..5c08880 100644 --- a/nextflow.config +++ b/nextflow.config @@ -271,7 +271,7 @@ manifest { description = """Single-cell/nuclei pipeline for data derived from Oxford Nanopore""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.0.0dev' + version = '0.1.0dev' doi = '' } diff --git a/workflows/scnanoseq.nf b/workflows/scnanoseq.nf index dd0242d..01352bd 100644 --- a/workflows/scnanoseq.nf +++ b/workflows/scnanoseq.nf @@ -210,10 +210,15 @@ workflow SCNANOSEQ { // MODULE: NanoComp for FastQ files // + ch_nanocomp_fastq_html = Channel.empty() + ch_nanocomp_fastq_txt = Channel.empty() if (!params.skip_qc && !params.skip_fastq_nanocomp) { ch_nanocomp_fastqs = ch_cat_fastq.collect{it[1]} NANOCOMP_FASTQ ( ch_nanocomp_fastqs ) + ch_nanocomp_fastq_html = NANOCOMP_FASTQ.out.html + ch_nanocomp_fastq_txt = NANOCOMP_FASTQ.out.txt + ch_versions = ch_versions.mix( NANOCOMP_FASTQ.out.versions ) } @@ -437,11 +442,16 @@ workflow SCNANOSEQ { // // MODULE: NanoComp for BAM files (unfiltered for QC purposes) // + ch_nanocomp_bam_html = Channel.empty() + ch_nanocomp_bam_txt = Channel.empty() if (!params.skip_qc && !params.skip_bam_nanocomp) { ch_nanocomp_bams = ch_minimap_sorted_bam.collect{it[1]} NANOCOMP_BAM ( ch_nanocomp_bams ) + + ch_nanocomp_bam_html = NANOCOMP_BAM.out.html + ch_nanocomp_bam_txt = NANOCOMP_BAM.out.txt ch_versions = ch_versions.mix( NANOCOMP_BAM.out.versions ) } @@ -492,13 +502,16 @@ workflow SCNANOSEQ { ch_dedup_sorted_bam = ch_corrected_sorted_bam ch_dedup_sorted_bam_bai = ch_corrected_sorted_bai ch_dedup_sorted_flagstat = ch_corrected_sorted_flagstat + ch_dedup_log = Channel.empty() if (!params.skip_dedup) { // // MODULE: Umitools Dedup // UMITOOLS_DEDUP ( ch_corrected_sorted_bam.join(ch_corrected_sorted_bai, by: [0]), true ) + ch_dedup_bam = UMITOOLS_DEDUP.out.bam + ch_dedup_log = UMITOOLS_DEDUP.out.log ch_versions = ch_versions.mix(UMITOOLS_DEDUP.out.versions) // SUBWORKFLOW: BAM_SORT_STATS_SAMTOOLS @@ -568,6 +581,8 @@ workflow SCNANOSEQ { ch_multiqc_rawqc_files = ch_multiqc_rawqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([])) ch_multiqc_rawqc_files = ch_multiqc_rawqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_rawqc_files = ch_multiqc_rawqc_files.mix(ch_fastqc_multiqc_pretrim.collect().ifEmpty([])) + ch_multiqc_rawqc_files = ch_multiqc_rawqc_files.mix(ch_nanocomp_fastq_html.collect().ifEmpty([])) + ch_multiqc_rawqc_files = ch_multiqc_rawqc_files.mix(ch_nanocomp_fastq_txt.collect().ifEmpty([])) MULTIQC_RAWQC ( ch_multiqc_rawqc_files.collect(), @@ -590,18 +605,23 @@ workflow SCNANOSEQ { ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_fastqc_multiqc_postrim.collect().ifEmpty([])) ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_fastqc_multiqc_postextract.collect().ifEmpty([])) + + ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_nanocomp_bam_html.collect().ifEmpty([])) + ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_nanocomp_bam_txt.collect().ifEmpty([])) ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_minimap_sorted_stats.collect{it[1]}.ifEmpty([])) ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_minimap_sorted_flagstat.collect{it[1]}.ifEmpty([])) ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_minimap_sorted_idxstats.collect{it[1]}.ifEmpty([])) - ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_corrected_sorted_stats.collect{it[1]}.ifEmpty([])) + //ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_corrected_sorted_stats.collect{it[1]}.ifEmpty([])) ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_corrected_sorted_flagstat.collect{it[1]}.ifEmpty([])) ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_corrected_sorted_idxstats.collect{it[1]}.ifEmpty([])) - ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_dedup_sorted_stats.collect{it[1]}.ifEmpty([])) + //ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_dedup_sorted_stats.collect{it[1]}.ifEmpty([])) ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_dedup_sorted_flagstat.collect{it[1]}.ifEmpty([])) ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_dedup_sorted_idxstats.collect{it[1]}.ifEmpty([])) + + ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_dedup_log.collect{it[1]}.ifEmpty([])) ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_gene_stats_combined.collect().ifEmpty([])) ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_transcript_stats_combined.collect().ifEmpty([]))