From 81e6390e860679737a24ccad84410a090811a5dd Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Mon, 23 Oct 2023 10:06:48 +0100 Subject: [PATCH 1/4] Add more collect --- workflows/cutandrun.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/cutandrun.nf b/workflows/cutandrun.nf index c2a7ad7d..146dcdb0 100644 --- a/workflows/cutandrun.nf +++ b/workflows/cutandrun.nf @@ -380,8 +380,8 @@ workflow CUTANDRUN { ch_samtools_bam, ch_samtools_bai, params.dedup_target_reads, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fasta_index + PREPARE_GENOME.out.fasta.collect(), + PREPARE_GENOME.out.fasta_index.collect() ) ch_samtools_bam = DEDUPLICATE_PICARD.out.bam ch_samtools_bai = DEDUPLICATE_PICARD.out.bai @@ -418,8 +418,8 @@ workflow CUTANDRUN { DEDUPLICATE_LINEAR ( ch_samtools_bam, ch_samtools_bai, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fasta_index, + PREPARE_GENOME.out.fasta.collect(), + PREPARE_GENOME.out.fasta_index.collect(), params.dedup_target_reads, ch_linear_duplication_header_multiqc ) @@ -450,7 +450,7 @@ workflow CUTANDRUN { ch_samtools_bam, ch_samtools_bai, PREPARE_GENOME.out.chrom_sizes.collect(), - ch_dummy_file, + ch_dummy_file.collect(), params.normalisation_mode, ch_metadata_bt2_spikein ) From b49a6f9cc252d30f63ae84d6a6e73547d8b6e0c5 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Mon, 23 Oct 2023 10:27:00 +0100 Subject: [PATCH 2/4] debug --- subworkflows/local/prepare_peakcalling.nf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/subworkflows/local/prepare_peakcalling.nf b/subworkflows/local/prepare_peakcalling.nf index c59dd287..93252ba4 100644 --- a/subworkflows/local/prepare_peakcalling.nf +++ b/subworkflows/local/prepare_peakcalling.nf @@ -55,6 +55,8 @@ workflow PREPARE_PEAKCALLING { //ch_bam_scale_factor | view } + ch_bam_scale_factor | view + if (norm_mode == "Spikein" || norm_mode == "None") { /* * MODULE: Convert bam files to bedgraph From 155c4dd630175d677b1b28a17b64a8c45e477e8d Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Mon, 23 Oct 2023 16:28:08 +0100 Subject: [PATCH 3/4] debug --- workflows/cutandrun.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/cutandrun.nf b/workflows/cutandrun.nf index 146dcdb0..10d48050 100644 --- a/workflows/cutandrun.nf +++ b/workflows/cutandrun.nf @@ -450,7 +450,7 @@ workflow CUTANDRUN { ch_samtools_bam, ch_samtools_bai, PREPARE_GENOME.out.chrom_sizes.collect(), - ch_dummy_file.collect(), + ch_dummy_file, params.normalisation_mode, ch_metadata_bt2_spikein ) From bae0b9286dd7064d48ae33839c47145b4cfe7742 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Mon, 23 Oct 2023 16:29:30 +0100 Subject: [PATCH 4/4] Remove debug --- subworkflows/local/prepare_peakcalling.nf | 2 -- 1 file changed, 2 deletions(-) diff --git a/subworkflows/local/prepare_peakcalling.nf b/subworkflows/local/prepare_peakcalling.nf index 93252ba4..c59dd287 100644 --- a/subworkflows/local/prepare_peakcalling.nf +++ b/subworkflows/local/prepare_peakcalling.nf @@ -55,8 +55,6 @@ workflow PREPARE_PEAKCALLING { //ch_bam_scale_factor | view } - ch_bam_scale_factor | view - if (norm_mode == "Spikein" || norm_mode == "None") { /* * MODULE: Convert bam files to bedgraph