Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat: add remaining test datasets from encode #215

Merged
merged 2 commits into from
Nov 27, 2024
Merged

feat: add remaining test datasets from encode #215

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
a4e6f47
feat: add remaining test datasets from encode
kelly-sovacool Nov 26, 2024
c591e84
chore: update CHANGELOG.md
kelly-sovacool Nov 27, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down
8 changes: 8 additions & 0 deletions assets/samplesheet_human.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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,,
3 changes: 1 addition & 2 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down
Loading