From a4e6f477ff5e610c250884b524c1d2bfcc291462 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Mon, 25 Nov 2024 22:00:00 -0500 Subject: [PATCH 1/2] feat: add remaining test datasets from encode resolves #165 --- assets/samplesheet_human.csv | 8 ++++++++ main.nf | 3 +-- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/assets/samplesheet_human.csv b/assets/samplesheet_human.csv index 96f00fc..e904ff8 100644 --- a/assets/samplesheet_human.csv +++ b/assets/samplesheet_human.csv @@ -11,3 +11,11 @@ fastq_1,fastq_2,sample,rep,antibody,control /data/CCBR_Pipeliner/testdata/CHAMPAGNE/human/SRR14638304.fastq.gz,,A549_JUN_INPUT,1,, /data/CCBR_Pipeliner/testdata/CHAMPAGNE/human/SRR14638305.fastq.gz,,A549_JUN_INPUT,2,, /data/CCBR_Pipeliner/testdata/CHAMPAGNE/human/SRR14638306.fastq.gz,,A549_JUN_INPUT,3,, +/data/CCBR_Pipeliner/testdata/CHAMPAGNE/human/ENCFF391TRF_ENCFF822KCO.fastq.gz,,BLaER1_H3K4me3,1,H3K4me3,BLaER1_INPUT +/data/CCBR_Pipeliner/testdata/CHAMPAGNE/human/ENCFF989TVW.fastq.gz,,BLaER1_H3K4me3,2,H3K4me3,BLaER1_INPUT +/data/CCBR_Pipeliner/testdata/CHAMPAGNE/human/ENCFF097DJJ_ENCFF815UIL.fastq.gz,,BLaER1_H3K27ac,1,H3K27ac,BLaER1_INPUT +/data/CCBR_Pipeliner/testdata/CHAMPAGNE/human/ENCFF161DOP.fastq.gz,,BLaER1_H3K27ac,2,H3K27ac,BLaER1_INPUT +/data/CCBR_Pipeliner/testdata/CHAMPAGNE/human/ENCFF963ONJ.fastq.gz,,BLaER1_H3K36me3,1,H3K36me3,BLaER1_INPUT +/data/CCBR_Pipeliner/testdata/CHAMPAGNE/human/ENCFF686GPG.fastq.gz,,BLaER1_H3K36me3,2,H3K36me3,BLaER1_INPUT +/data/CCBR_Pipeliner/testdata/CHAMPAGNE/human/ENCFF259JCU.fastq.gz,,BLaER1_INPUT,1,, +/data/CCBR_Pipeliner/testdata/CHAMPAGNE/human/ENCFF622MZI.fastq.gz,,BLaER1_INPUT,2,, diff --git a/main.nf b/main.nf index 3f79ddc..dd41d9e 100644 --- a/main.nf +++ b/main.nf @@ -72,9 +72,8 @@ workflow { } workflow CHIPSEQ { - INPUT_CHECK(file(params.input, checkIfExists: true), params.seq_center, contrast_sheet) + raw_fastqs = INPUT_CHECK(file(params.input, checkIfExists: true), params.seq_center, contrast_sheet).reads - INPUT_CHECK.out.reads.set { raw_fastqs } CUTADAPT(raw_fastqs).reads | POOL_INPUTS trimmed_fastqs = POOL_INPUTS.out.reads From c591e8480afa8e1d4951fd742190688ca1483c5b Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Wed, 27 Nov 2024 12:18:47 -0500 Subject: [PATCH 2/2] chore: update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0d4adda..9b756c4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,7 @@ - The CHAMPAGNE nextflow workflow now has a version entry in `nextflow.config`, in compliance with nf-core. (#213, @kelly-sovacool) - Pool input (control) reads of the same sample name by default. Any inputs that should not be pooled must have different sample names in the samplesheet. (#214, @kelly-sovacool) +- Add histone samples to the `test_human` dataset. (#215, @kelly-sovacool) ## CHAMPAGNE 0.4.0