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Fix nf-core lint
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‎.github/PULL_REQUEST_TEMPLATE.md

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@@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/chip
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- [ ] If you've fixed a bug or added code that should be tested, add tests!
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- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/chipseq/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/chipseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
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- [ ] Make sure your code lints (`nf-core lint`).
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- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir <OUTDIR>`).
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- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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- [ ] Usage Documentation in `docs/usage.md` is updated.
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- [ ] Output Documentation in `docs/output.md` is updated.
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- [ ] `CHANGELOG.md` is updated.

‎.nf-core.yml

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repository_type: pipeline
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lint:
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files_unchanged:
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- .github/workflows/branch.yml
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- .github/workflows/linting_comment.yml
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- .github/workflows/linting.yml
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- .github/PULL_REQUEST_TEMPLATE.md
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- bin/check_samplesheet.py
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repository_type: pipeline

‎LICENSE

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MIT License
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Copyright (c) Philip Ewels, Jose Espinosa-Carrasco, Harshil Patel
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Copyright (c) Espinosa-Carrasco J, Patel H, Wang C, Ewels P
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal

‎modules.json

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"homePage": "https://github.com/nf-core/chipseq",
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"repos": {
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"nf-core/modules": {
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"bowtie2/align": {
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"git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c"
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},
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"bowtie2/build": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"bwa/index": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"bwa/mem": {
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"git_sha": "4f5274c3de0c9521f5033893ff61057a74c45ba9"
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},
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"chromap/chromap": {
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"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
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},
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"chromap/index": {
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"git_sha": "dbb46c9b635080b132bab4b8d5b9a14f0d1c22e7"
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},
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"custom/dumpsoftwareversions": {
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"git_sha": "e5b44499efcf6f7fb24874886bac60591c5d94dd"
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},
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"custom/getchromsizes": {
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"git_sha": "213403187932dbbdd936a04474cc8cd8abae7a08"
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},
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"deeptools/computematrix": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"deeptools/plotfingerprint": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"deeptools/plotheatmap": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"deeptools/plotprofile": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"fastqc": {
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"git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
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},
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"gffread": {
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},
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"gunzip": {
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},
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"homer/annotatepeaks": {
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"git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
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},
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"khmer/uniquekmers": {
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"git_sha": "82fdff4fb4ce6cafcc028a7503da835427f35352"
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},
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"macs2/callpeak": {
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"git_sha": "f0800157544a82ae222931764483331a81812012"
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},
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"phantompeakqualtools": {
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"git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
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},
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"picard/collectmultiplemetrics": {
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"git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
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},
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"picard/markduplicates": {
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"git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
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},
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"picard/mergesamfiles": {
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"git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
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},
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"preseq/lcextrap": {
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"git_sha": "7111e571cc5b6069de4673cd6165af680f17b4d7"
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},
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"samtools/flagstat": {
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"git_sha": "ecece498f10b47b7c9d06f53a310cea5811b4c5f"
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},
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"samtools/idxstats": {
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"git_sha": "ecece498f10b47b7c9d06f53a310cea5811b4c5f"
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},
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"samtools/index": {
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"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
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},
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"samtools/sort": {
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"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
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},
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"samtools/stats": {
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"git_sha": "f48a24770e24358e58de66e9b805a70d77cd154b"
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},
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"subread/featurecounts": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"trimgalore": {
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"git_sha": "85ec13ff1fc2196c5a507ea497de468101baabed"
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},
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"ucsc/bedgraphtobigwig": {
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"git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
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},
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"untar": {
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"git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5"
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"git_url": "https://github.com/nf-core/modules.git",
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"modules": {
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"bowtie2/align": {
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"branch": "master",
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"git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c"
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},
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"bowtie2/build": {
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"branch": "master",
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"bwa/index": {
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"branch": "master",
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"bwa/mem": {
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"branch": "master",
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"git_sha": "4f5274c3de0c9521f5033893ff61057a74c45ba9"
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},
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"chromap/chromap": {
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"branch": "master",
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"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
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},
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"chromap/index": {
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"branch": "master",
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"git_sha": "dbb46c9b635080b132bab4b8d5b9a14f0d1c22e7"
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},
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"custom/dumpsoftwareversions": {
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"branch": "master",
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"git_sha": "e5b44499efcf6f7fb24874886bac60591c5d94dd"
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},
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"custom/getchromsizes": {
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"branch": "master",
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"git_sha": "213403187932dbbdd936a04474cc8cd8abae7a08"
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},
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"deeptools/computematrix": {
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"branch": "master",
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"deeptools/plotfingerprint": {
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"branch": "master",
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"deeptools/plotheatmap": {
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"branch": "master",
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"deeptools/plotprofile": {
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"branch": "master",
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"fastqc": {
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"branch": "master",
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"git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
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},
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"gffread": {
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"branch": "master",
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "fa37e0662690c4ec4260dae282fbce08777503e6"
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},
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"homer/annotatepeaks": {
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"branch": "master",
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"git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
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},
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"khmer/uniquekmers": {
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"branch": "master",
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"git_sha": "82fdff4fb4ce6cafcc028a7503da835427f35352"
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},
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"macs2/callpeak": {
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"branch": "master",
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"git_sha": "f0800157544a82ae222931764483331a81812012"
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},
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"phantompeakqualtools": {
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"branch": "master",
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"git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
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},
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"picard/collectmultiplemetrics": {
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"branch": "master",
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"git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
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},
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"picard/markduplicates": {
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"branch": "master",
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"git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
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},
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"picard/mergesamfiles": {
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"branch": "master",
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"git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
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},
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"preseq/lcextrap": {
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"branch": "master",
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"git_sha": "7111e571cc5b6069de4673cd6165af680f17b4d7"
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},
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"samtools/flagstat": {
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"branch": "master",
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"git_sha": "ecece498f10b47b7c9d06f53a310cea5811b4c5f"
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},
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"samtools/idxstats": {
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"branch": "master",
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"git_sha": "ecece498f10b47b7c9d06f53a310cea5811b4c5f"
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},
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"samtools/index": {
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"branch": "master",
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"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
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},
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"samtools/sort": {
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"branch": "master",
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"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
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},
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"samtools/stats": {
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"branch": "master",
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"git_sha": "f48a24770e24358e58de66e9b805a70d77cd154b"
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},
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"subread/featurecounts": {
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"branch": "master",
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"trimgalore": {
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"branch": "master",
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"git_sha": "85ec13ff1fc2196c5a507ea497de468101baabed"
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},
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"ucsc/bedgraphtobigwig": {
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"branch": "master",
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"git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
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},
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"untar": {
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"branch": "master",
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"git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5"
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}
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}
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}
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}

‎nextflow.config

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manifest {
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name = 'nf-core/chipseq'
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author = 'Jose Espinosa-Carrasco, Harshil Patel, Philip Ewels'
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author = 'Espinosa-Carrasco J, Patel H, Wang C, Ewels P'
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homePage = 'https://github.com/nf-core/chipseq'
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description = 'ChIP-seq peak-calling and differential analysis pipeline.'
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mainScript = 'main.nf'

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