diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index f3dbd188d0fd31c93bd61a759a2901b35d6e6d0e..8da27af0eb9a6017271d057b39940493b3ac4bc4 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/chip
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] 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.
- [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
diff --git a/.nf-core.yml b/.nf-core.yml
index f1d2ac4eda43d6ae7ee39d53260ffb5b5a989762..b1a7f0e91809e0f51e78b49d1f1d8557c79fdb79 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,8 +1 @@
-repository_type: pipeline
-lint:
- files_unchanged:
- - .github/workflows/branch.yml
- - .github/workflows/linting_comment.yml
- - .github/workflows/linting.yml
- - .github/PULL_REQUEST_TEMPLATE.md
- - bin/check_samplesheet.py
+repository_type: pipeline
\ No newline at end of file
diff --git a/LICENSE b/LICENSE
index e6309f5746d185662c6fcee3d18fb99759f19cf2..9ddb87a26277f67fb56d71faa4d1f1f7633ddfe3 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
MIT License
-Copyright (c) Philip Ewels, Jose Espinosa-Carrasco, Harshil Patel
+Copyright (c) Espinosa-Carrasco J, Patel H, Wang C, Ewels P
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
diff --git a/modules.json b/modules.json
index ad30c80a2fcefa8ec0063233abb612b4d7dccf7b..81c94b44a341e1c2ffead5e659408c3b936d5399 100644
--- a/modules.json
+++ b/modules.json
@@ -3,101 +3,136 @@
"homePage": "https://github.com/nf-core/chipseq",
"repos": {
"nf-core/modules": {
- "bowtie2/align": {
- "git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c"
- },
- "bowtie2/build": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "bwa/index": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "bwa/mem": {
- "git_sha": "4f5274c3de0c9521f5033893ff61057a74c45ba9"
- },
- "chromap/chromap": {
- "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
- },
- "chromap/index": {
- "git_sha": "dbb46c9b635080b132bab4b8d5b9a14f0d1c22e7"
- },
- "custom/dumpsoftwareversions": {
- "git_sha": "e5b44499efcf6f7fb24874886bac60591c5d94dd"
- },
- "custom/getchromsizes": {
- "git_sha": "213403187932dbbdd936a04474cc8cd8abae7a08"
- },
- "deeptools/computematrix": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "deeptools/plotfingerprint": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "deeptools/plotheatmap": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "deeptools/plotprofile": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "fastqc": {
- "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
- },
- "gffread": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "gunzip": {
- "git_sha": "fa37e0662690c4ec4260dae282fbce08777503e6"
- },
- "homer/annotatepeaks": {
- "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
- },
- "khmer/uniquekmers": {
- "git_sha": "82fdff4fb4ce6cafcc028a7503da835427f35352"
- },
- "macs2/callpeak": {
- "git_sha": "f0800157544a82ae222931764483331a81812012"
- },
- "phantompeakqualtools": {
- "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
- },
- "picard/collectmultiplemetrics": {
- "git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
- },
- "picard/markduplicates": {
- "git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
- },
- "picard/mergesamfiles": {
- "git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
- },
- "preseq/lcextrap": {
- "git_sha": "7111e571cc5b6069de4673cd6165af680f17b4d7"
- },
- "samtools/flagstat": {
- "git_sha": "ecece498f10b47b7c9d06f53a310cea5811b4c5f"
- },
- "samtools/idxstats": {
- "git_sha": "ecece498f10b47b7c9d06f53a310cea5811b4c5f"
- },
- "samtools/index": {
- "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
- },
- "samtools/sort": {
- "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
- },
- "samtools/stats": {
- "git_sha": "f48a24770e24358e58de66e9b805a70d77cd154b"
- },
- "subread/featurecounts": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "trimgalore": {
- "git_sha": "85ec13ff1fc2196c5a507ea497de468101baabed"
- },
- "ucsc/bedgraphtobigwig": {
- "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
- },
- "untar": {
- "git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5"
+ "git_url": "https://github.com/nf-core/modules.git",
+ "modules": {
+ "bowtie2/align": {
+ "branch": "master",
+ "git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c"
+ },
+ "bowtie2/build": {
+ "branch": "master",
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+ },
+ "bwa/index": {
+ "branch": "master",
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+ },
+ "bwa/mem": {
+ "branch": "master",
+ "git_sha": "4f5274c3de0c9521f5033893ff61057a74c45ba9"
+ },
+ "chromap/chromap": {
+ "branch": "master",
+ "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+ },
+ "chromap/index": {
+ "branch": "master",
+ "git_sha": "dbb46c9b635080b132bab4b8d5b9a14f0d1c22e7"
+ },
+ "custom/dumpsoftwareversions": {
+ "branch": "master",
+ "git_sha": "e5b44499efcf6f7fb24874886bac60591c5d94dd"
+ },
+ "custom/getchromsizes": {
+ "branch": "master",
+ "git_sha": "213403187932dbbdd936a04474cc8cd8abae7a08"
+ },
+ "deeptools/computematrix": {
+ "branch": "master",
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+ },
+ "deeptools/plotfingerprint": {
+ "branch": "master",
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+ },
+ "deeptools/plotheatmap": {
+ "branch": "master",
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+ },
+ "deeptools/plotprofile": {
+ "branch": "master",
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+ },
+ "fastqc": {
+ "branch": "master",
+ "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
+ },
+ "gffread": {
+ "branch": "master",
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+ },
+ "gunzip": {
+ "branch": "master",
+ "git_sha": "fa37e0662690c4ec4260dae282fbce08777503e6"
+ },
+ "homer/annotatepeaks": {
+ "branch": "master",
+ "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
+ },
+ "khmer/uniquekmers": {
+ "branch": "master",
+ "git_sha": "82fdff4fb4ce6cafcc028a7503da835427f35352"
+ },
+ "macs2/callpeak": {
+ "branch": "master",
+ "git_sha": "f0800157544a82ae222931764483331a81812012"
+ },
+ "phantompeakqualtools": {
+ "branch": "master",
+ "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
+ },
+ "picard/collectmultiplemetrics": {
+ "branch": "master",
+ "git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
+ },
+ "picard/markduplicates": {
+ "branch": "master",
+ "git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
+ },
+ "picard/mergesamfiles": {
+ "branch": "master",
+ "git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
+ },
+ "preseq/lcextrap": {
+ "branch": "master",
+ "git_sha": "7111e571cc5b6069de4673cd6165af680f17b4d7"
+ },
+ "samtools/flagstat": {
+ "branch": "master",
+ "git_sha": "ecece498f10b47b7c9d06f53a310cea5811b4c5f"
+ },
+ "samtools/idxstats": {
+ "branch": "master",
+ "git_sha": "ecece498f10b47b7c9d06f53a310cea5811b4c5f"
+ },
+ "samtools/index": {
+ "branch": "master",
+ "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+ },
+ "samtools/sort": {
+ "branch": "master",
+ "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+ },
+ "samtools/stats": {
+ "branch": "master",
+ "git_sha": "f48a24770e24358e58de66e9b805a70d77cd154b"
+ },
+ "subread/featurecounts": {
+ "branch": "master",
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+ },
+ "trimgalore": {
+ "branch": "master",
+ "git_sha": "85ec13ff1fc2196c5a507ea497de468101baabed"
+ },
+ "ucsc/bedgraphtobigwig": {
+ "branch": "master",
+ "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
+ },
+ "untar": {
+ "branch": "master",
+ "git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5"
+ }
}
}
}
diff --git a/nextflow.config b/nextflow.config
index 58cea5bfa6a7336b3f37bf80599889cefcd7a483..c2e329b6f087df787128aa4c8bf195efa409e59c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -230,7 +230,7 @@ dag {
manifest {
name = 'nf-core/chipseq'
- author = 'Jose Espinosa-Carrasco, Harshil Patel, Philip Ewels'
+ author = 'Espinosa-Carrasco J, Patel H, Wang C, Ewels P'
homePage = 'https://github.com/nf-core/chipseq'
description = 'ChIP-seq peak-calling and differential analysis pipeline.'
mainScript = 'main.nf'