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fix: output tagalign files #313

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fix: output tagalign files #313

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07162f4
feat: output tagalign files
kelly-sovacool Feb 12, 2026
b25f8df
ci: 📑 update contributors page with .github/contributors.py
github-actions[bot] Mar 3, 2026
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4 changes: 2 additions & 2 deletions assets/samplesheet_test.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -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,,,
2 changes: 1 addition & 1 deletion docs/devs/contributors.md
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Expand Up @@ -3,6 +3,6 @@
| | | |
| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| <a href='https://github.com/kelly-sovacool' title='Kelly Sovacool, PhD' style='display: inline-block; text-align: center;'><img src='https://avatars.githubusercontent.com/u/17768269?v=4' alt='Kelly Sovacool, PhD' style='border-radius: 50%; width: 30%;'><br>Kelly Sovacool, PhD</a> | <a href='https://github.com/apps/github-actions' title='github-actions[bot]' style='display: inline-block; text-align: center;'><img src='https://avatars.githubusercontent.com/in/15368?v=4' alt='github-actions[bot]' style='border-radius: 50%; width: 30%;'><br>github-actions[bot]</a> | <a href='https://github.com/slsevilla' title='Samantha' style='display: inline-block; text-align: center;'><img src='https://avatars.githubusercontent.com/u/20726305?v=4' alt='Samantha' style='border-radius: 50%; width: 30%;'><br>Samantha</a> |
| <a href='https://github.com/kopardev' title='Vishal Koparde, PhD' style='display: inline-block; text-align: center;'><img src='https://avatars.githubusercontent.com/u/1882209?v=4' alt='Vishal Koparde, PhD' style='border-radius: 50%; width: 30%;'><br>Vishal Koparde, PhD</a> |
| <a href='https://github.com/kopardev' title='Vishal Koparde, PhD' style='display: inline-block; text-align: center;'><img src='https://avatars.githubusercontent.com/u/1882209?v=4' alt='Vishal Koparde, PhD' style='border-radius: 50%; width: 30%;'><br>Vishal Koparde, PhD</a> | <a href='https://github.com/apps/copilot-swe-agent' title='Copilot' style='display: inline-block; text-align: center;'><img src='https://avatars.githubusercontent.com/in/1143301?v=4' alt='Copilot' style='border-radius: 50%; width: 30%;'><br>Copilot</a> |

View the [contributors graph on GitHub](https://github.com/CCBR/CHAMPAGNE/graphs/contributors) for more details.
8 changes: 6 additions & 2 deletions main.nf
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Expand Up @@ -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
Expand Down Expand Up @@ -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/"}
}
Expand Down