diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 9e36cfd31290791aaa5bb9307fe33432acfb6b91..078248e142a984d938145ff04fd4e14a7e5ba4e8 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -46,7 +46,7 @@ These tests are run both with the latest available version of `Nextflow` and als
## Patch
-: warning: Only in the unlikely and regretful event of a release happening with a bug.
+:warning: Only in the unlikely and regretful event of a release happening with a bug.
* On your own fork, make a new branch `patch` based on `upstream/master`.
* Fix the bug, and bump version (X.Y.Z+1).
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 902758a1ca194c9b9afe45b21f71f4a88934ff3a..26d2e7e9f9223900ddc066163f442f821d1a62f3 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -21,7 +21,7 @@ jobs:
run: conda install -c conda-forge awscli
- name: Start AWS batch job
# TODO nf-core: You can customise AWS full pipeline tests as required
- # Add full size test data (but still relatively small datasets for few samples)
+ # Add full size test data (but still relatively small datasets for few samples)
# on the `test_full.config` test runs with only one set of parameters
# Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
env:
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 17fa32f0693c60ab733e83d8b92037675eddc3f7..04dbb3d4b77e32d8ff4e3fa7f0ba17046111d1a3 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -17,6 +17,7 @@ jobs:
# If the above check failed, post a comment on the PR explaining the failure
+ # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
- name: Post PR comment
if: failure()
uses: mshick/add-pr-comment@v1
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index eb66c14490925a762b8d5c3fb1d07a658884936c..8e8d5bbcf72289280dca21cdbe7623cd063d6f86 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -57,5 +57,12 @@ jobs:
GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
- run: nf-core lint ${GITHUB_WORKSPACE}
+ run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE}
+
+ - name: Upload linting log file artifact
+ if: ${{ always() }}
+ uses: actions/upload-artifact@v2
+ with:
+ name: linting-log-file
+ path: lint_log.txt
diff --git a/.github/workflows/push_dockerhub.yml b/.github/workflows/push_dockerhub.yml
index 31cf786cbe186a6aff9931b899d74643f7eff5b9..280f8ba5b9fa9581c0954275cf77629492aa5c7f 100644
--- a/.github/workflows/push_dockerhub.yml
+++ b/.github/workflows/push_dockerhub.yml
@@ -8,32 +8,33 @@ on:
release:
types: [published]
-push_dockerhub:
- name: Push new Docker image to Docker Hub
- runs-on: ubuntu-latest
- # Only run for the nf-core repo, for releases and merged PRs
- if: ${{ github.repository == 'nf-core/hic' }}
- env:
- DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
- DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
- steps:
- - name: Check out pipeline code
- uses: actions/checkout@v2
+jobs:
+ push_dockerhub:
+ name: Push new Docker image to Docker Hub
+ runs-on: ubuntu-latest
+ # Only run for the nf-core repo, for releases and merged PRs
+ if: ${{ github.repository == 'nf-core/hic' }}
+ env:
+ DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+ DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
+ steps:
+ - name: Check out pipeline code
+ uses: actions/checkout@v2
- - name: Build new docker image
- run: docker build --no-cache . -t nfcore/hic:latest
+ - name: Build new docker image
+ run: docker build --no-cache . -t nfcore/hic:latest
- - name: Push Docker image to DockerHub (dev)
- if: ${{ github.event_name == 'push' }}
- run: |
- echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
- docker tag nfcore/hic:latest nfcore/hic:dev
- docker push nfcore/hic:dev
+ - name: Push Docker image to DockerHub (dev)
+ if: ${{ github.event_name == 'push' }}
+ run: |
+ echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+ docker tag nfcore/hic:latest nfcore/hic:dev
+ docker push nfcore/hic:dev
- - name: Push Docker image to DockerHub (release)
- if: ${{ github.event_name == 'release' }}
- run: |
- echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
- docker push nfcore/hic:latest
- docker tag nfcore/hic:latest nfcore/hic:${{ github.event.release.tag_name }}
- docker push nfcore/hic:${{ github.event.release.tag_name }}
+ - name: Push Docker image to DockerHub (release)
+ if: ${{ github.event_name == 'release' }}
+ run: |
+ echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+ docker push nfcore/hic:latest
+ docker tag nfcore/hic:latest nfcore/hic:${{ github.event.release.tag_name }}
+ docker push nfcore/hic:${{ github.event.release.tag_name }}
diff --git a/Dockerfile b/Dockerfile
index ae1294d64046e290db7497108a722267a9ff92a4..f7e704c8df0c2008f3647406381ee8225ed1eeb0 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM nfcore/base:1.10.1
+FROM nfcore/base:1.10.2
LABEL authors="Nicolas Servant" \
description="Docker image containing all software requirements for the nf-core/hic pipeline"
diff --git a/conf/test_full.config b/conf/test_full.config
index 31742b37c7fb0a74ea920925140fdfeac91bc22a..921372eec05fe6147c540a39463c54f0ebf09bce 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -15,7 +15,7 @@ params {
// TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
// TODO nf-core: Give any required params for the test so that command line flags are not needed
single_end = false
- readPaths = [
+ input_paths = [
['Testdata', ['https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R1.tiny.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R2.tiny.fastq.gz']],
['SRR389222', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']]
]
diff --git a/docs/usage.md b/docs/usage.md
index 636d70cd8854be60394bf420663f4840684ea421..21419157b7c30126ec0eca6b8188284dcbb7325a 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -80,7 +80,7 @@ You can also supply a run name to resume a specific run: `-resume [run-name]`. U
### `-c`
-Specify the path to a specific config file (this is a core NextFlow command). See the [nf-core website documentation](https://nf-co.re/usage/configuration) for more information.
+Specify the path to a specific config file (this is a core Nextflow command). See the [nf-core website documentation](https://nf-co.re/usage/configuration) for more information.
#### Custom resource requests
diff --git a/main.nf b/main.nf
index 5059f70997f6f297e5e30be136734f01e4a58a08..7a83f8e2316eb0c059a885b3eee004591a46a041 100644
--- a/main.nf
+++ b/main.nf
@@ -127,7 +127,7 @@ def summary = [:]
if (workflow.revision) summary['Pipeline Release'] = workflow.revision
summary['Run Name'] = custom_runName ?: workflow.runName
// TODO nf-core: Report custom parameters here
-summary['Reads'] = params.input
+summary['Input'] = params.input
summary['Fasta Ref'] = params.fasta
summary['Data Type'] = params.single_end ? 'Single-End' : 'Paired-End'
summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"