Fix nf-core lint

.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.

.nf-core.yml

-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

LICENSE

 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

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"
+                }
             }
         }
     }

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'