diff --git a/assets/samplesheet_test.csv b/assets/samplesheet_test.csv index 0244f29c..d303f4fc 100644 --- a/assets/samplesheet_test.csv +++ b/assets/samplesheet_test.csv @@ -3,5 +3,5 @@ SPT5_T0,1,https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testda SPT5_T0,2,https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822154_1.fastq.gz,,SPT5,SPT5_INPUT SPT5_T15,1,https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822157_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822157_2.fastq.gz,SPT5,SPT5_INPUT SPT5_T15,2,https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822158_1.fastq.gz,,SPT5,SPT5_INPUT -SPT5_INPUT,1,https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/testdata/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/testdata/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R2.fastq.gz,, -SPT5_INPUT,2,https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/testdata/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/testdata/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R2.fastq.gz,, +SPT5_INPUT,1,https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/testdata/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R1.fastq.gz,,, +SPT5_INPUT,2,https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/testdata/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R1.fastq.gz,,, diff --git a/docs/devs/contributors.md b/docs/devs/contributors.md index 323992cc..f13a17eb 100644 --- a/docs/devs/contributors.md +++ b/docs/devs/contributors.md @@ -3,6 +3,6 @@ | | | | | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Kelly Sovacool, PhD
Kelly Sovacool, PhD
| github-actions[bot]
github-actions[bot]
| Samantha
Samantha
| -| Vishal Koparde, PhD
Vishal Koparde, PhD
| +| Vishal Koparde, PhD
Vishal Koparde, PhD
| Copilot
Copilot
| View the [contributors graph on GitHub](https://github.com/CCBR/CHAMPAGNE/graphs/contributors) for more details. diff --git a/main.nf b/main.nf index 9a1b7b98..9801de18 100644 --- a/main.nf +++ b/main.nf @@ -305,7 +305,8 @@ workflow { deeptools_stats = ch_deeptools_stats multiqc_report = multiqc_report multiqc_inputs = ch_multiqc - align_bam = DEDUPLICATE.out.bam + dedup_bam = DEDUPLICATE.out.bam + dedup_tagalign = DEDUPLICATE.out.tag_align peaks = ch_peaks peaks_consensus = ch_peaks_consensus annot = ch_annot @@ -344,9 +345,12 @@ output { multiqc_inputs { path { inputs -> "qc/multiqc/inputs/" } } - align_bam { + dedup_bam { path { bam -> "align/bam/" } } + dedup_tagalign { + path { tagalign -> "align/tagalign/" } + } peaks { path { meta, peak, tool -> "peaks/${meta.tool}/replicates/"} }