feat: add remaining test datasets from encode (#215)

* feat: add remaining test datasets from encode resolves #165 * chore: update CHANGELOG.md
CCBR · Nov 27, 2024 · 8be081b · 8be081b
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diff --git 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
 

diff --git 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
@@ -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