From 9bc99b53a2d22099a7f9da1b394771d2d13872a6 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Tue, 23 Jan 2024 15:41:19 -0500 Subject: [PATCH 1/2] refactor: change last process name for better final output dir name --- subworkflows/CCBR/consensus_peaks/main.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/subworkflows/CCBR/consensus_peaks/main.nf b/subworkflows/CCBR/consensus_peaks/main.nf index 18b13d7..fd39ba9 100644 --- a/subworkflows/CCBR/consensus_peaks/main.nf +++ b/subworkflows/CCBR/consensus_peaks/main.nf @@ -1,7 +1,7 @@ include { CAT_CAT } from '../../../modules/CCBR/cat/cat/' include { SORT_BED } from '../../../modules/CCBR/sort/bed' include { BEDTOOLS_MERGE } from '../../../modules/CCBR/bedtools/merge/' -include { CUSTOM_FORMATMERGEDBED } from '../../../modules/CCBR/custom/formatmergedbed/' +include { CUSTOM_FORMATMERGEDBED as CONSENSUS_PEAKS_OUT } from '../../../modules/CCBR/custom/formatmergedbed/' include { CUSTOM_NORMALIZEPEAKS } from '../../../modules/CCBR/custom/normalizepeaks/' workflow CONSENSUS_PEAKS { @@ -32,14 +32,14 @@ workflow CONSENSUS_PEAKS { peaks_grouped | CAT_CAT SORT_BED( CAT_CAT.out.file_out ) BEDTOOLS_MERGE(SORT_BED.out.bed, ' -c 1,5,6,7,8,9 -o count,collapse,collapse,collapse,collapse,collapse ') - CUSTOM_FORMATMERGEDBED(BEDTOOLS_MERGE.out.bed) - consensus_peaks = CUSTOM_FORMATMERGEDBED.out.bed + CONSENSUS_PEAKS_OUT(BEDTOOLS_MERGE.out.bed) + consensus_peaks = CONSENSUS_PEAKS_OUT.out.bed ch_versions = ch_versions.mix( CAT_CAT.out.versions, SORT_BED.out.versions, BEDTOOLS_MERGE.out.versions, - CUSTOM_FORMATMERGEDBED.out.versions + CONSENSUS_PEAKS_OUT.out.versions ) emit: From f912c4476ea33554930337ad95b7e746237fc7a6 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Wed, 24 Jan 2024 10:04:35 -0500 Subject: [PATCH 2/2] test: new out dir --- tests/subworkflows/CCBR/consensus_peaks/test.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/subworkflows/CCBR/consensus_peaks/test.yml b/tests/subworkflows/CCBR/consensus_peaks/test.yml index 0031535..5b269b7 100644 --- a/tests/subworkflows/CCBR/consensus_peaks/test.yml +++ b/tests/subworkflows/CCBR/consensus_peaks/test.yml @@ -17,7 +17,7 @@ md5sum: 04ce00285f1960a006f13e5f90482ea1 - path: output/cat_cat/macs_broad.broadPeak md5sum: c5d73e727a10d2a32b139efcdd369f59 - - path: output/custom_formatmergedbed/macs_broad.sorted.merged.consensus.bed + - path: output/consensus_peaks_out/macs_broad.sorted.merged.consensus.bed md5sum: 4266c4e4fed0ceaaaf97ecd0a6baaec4 - path: output/sort_bed/macs_broad.sorted.bed md5sum: 7ea9a8ca2c6ad93dc7e7714016789559 @@ -45,9 +45,9 @@ md5sum: 64bdb72657a26b8bc963f9bd51f39565 - path: output/cat_cat/macs_narrow.bed md5sum: 3974447bc99fc4930b56e171e545bc14 - - path: output/custom_formatmergedbed/macs_broad.sorted.merged.consensus.bed + - path: output/consensus_peaks_out/macs_broad.sorted.merged.consensus.bed md5sum: 4f4d67389a8e327f21c0fd6d0d482780 - - path: output/custom_formatmergedbed/macs_narrow.sorted.merged.consensus.bed + - path: output/consensus_peaks_out/macs_narrow.sorted.merged.consensus.bed md5sum: 51fee8455d9357b659d7c463c26e8158 - path: output/custom_normalizepeaks/SPT5_T0_1_peaks.broadPeak.norm.bed md5sum: b330f110355268468fd775945de0e0d3 @@ -79,5 +79,5 @@ files: - path: output/bedtools_merge/macs_broad.sorted.merged.bed - path: output/cat_cat/macs_broad.broadPeak - - path: output/custom_formatmergedbed/macs_broad.sorted.merged.consensus.bed + - path: output/consensus_peaks_out/macs_broad.sorted.merged.consensus.bed - path: output/sort_bed/macs_broad.sorted.bed