From 7230095677ba87f5325ed7bd4d853b00ee4255fe Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Wed, 30 Oct 2024 10:31:25 +0000 Subject: [PATCH] have outputs separated --- subworkflows/local/starsolo.nf | 14 +++++--------- workflows/scrnaseq.nf | 4 +++- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/subworkflows/local/starsolo.nf b/subworkflows/local/starsolo.nf index d69ce9d9..4cbf7aea 100644 --- a/subworkflows/local/starsolo.nf +++ b/subworkflows/local/starsolo.nf @@ -54,16 +54,12 @@ workflow STARSOLO { ) ch_versions = ch_versions.mix(STAR_ALIGN.out.versions) - // generate channel of star counts with correct metadata - ch_star_counts = - STAR_ALIGN.out.raw_counts.map{ meta, files -> [meta + [input_type: 'raw'], files] } - .mix( STAR_ALIGN.out.filtered_counts.map{ meta, files -> [meta + [input_type: 'filtered'], files] } ) - - emit: ch_versions // get rid of meta for star index - star_result = STAR_ALIGN.out.tab - star_counts = ch_star_counts - for_multiqc = STAR_ALIGN.out.log_final.map{ meta, it -> it } + star_result = STAR_ALIGN.out.tab + star_counts = STAR_ALIGN.out.counts + raw_counts = STAR_ALIGN.out.raw_counts + filtered_counts = STAR_ALIGN.out.filtered_counts + for_multiqc = STAR_ALIGN.out.log_final.map{ meta, it -> it } } diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf index 61401185..f7bbe692 100644 --- a/workflows/scrnaseq.nf +++ b/workflows/scrnaseq.nf @@ -170,7 +170,9 @@ workflow SCRNASEQ { ) ch_versions = ch_versions.mix(STARSOLO.out.ch_versions) ch_multiqc_files = ch_multiqc_files.mix(STARSOLO.out.for_multiqc) - ch_mtx_matrices = STARSOLO.out.star_counts + ch_mtx_matrices = + STARSOLO.out.raw_counts.map{ meta, files -> [meta + [input_type: 'raw'], files] } + .mix( STARSOLO.out.filtered_counts.map{ meta, files -> [meta + [input_type: 'filtered'], files] } ) } // Run cellranger pipeline