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Prepare release 2.7.1 #374

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Jun 14, 2021
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0ce6802
chores: merge 2.7 to dev
maxulysse Jan 26, 2021
d56135d
chores: remove extra head tag
maxulysse Jan 26, 2021
31c43f2
fix: remove conflicts comments
maxulysse Jan 26, 2021
6fbcb67
chores: update CHANGELOG
maxulysse Jan 26, 2021
13def96
Merge pull request #333 from MaxUlysse/dev
maxulysse Jan 26, 2021
a1f11f0
Merge pull request #2 from nf-core/master
jfnavarro Feb 22, 2021
ac90102
Add Mutect2 tumor-only mode
jfnavarro Feb 22, 2021
f402d60
Update for Mutect2 and MSIsensor in tumor only mode
jfnavarro Feb 23, 2021
8a57b7a
Update for Mutect2 and MSIsensor in tumor only mode
jfnavarro Feb 23, 2021
9335338
Update
jfnavarro Feb 23, 2021
5f6af94
Update
jfnavarro Feb 23, 2021
4571ade
Update container
jfnavarro Feb 23, 2021
68929bc
Updading container for MSIsensor process
jfnavarro Feb 23, 2021
a1b880b
Update main.nf
jfnavarro Feb 23, 2021
89dbb6c
Retry tasks with exit code 247 for added memory
Feb 24, 2021
1cc5ceb
Mention new exit code in CHANGELOG
Feb 24, 2021
68ca38b
Merge branch 'dev' into patch-1
maxulysse Feb 24, 2021
192e5df
Update in msisensor tumor only
jfnavarro Feb 24, 2021
f365b81
Merge pull request #353 from BrunoGrandePhD/patch-1
maxulysse Feb 24, 2021
527fcd5
Container should be dev
jfnavarro Feb 24, 2021
52154b0
Correct name for Mutect2 tumor-only process
jfnavarro Feb 24, 2021
25113f1
Fix an issue with Mutect2
jfnavarro Mar 2, 2021
eb0f8b4
feat: add contaminationAdjustement option for Control-FREEC
maxulysse Mar 8, 2021
e91a68a
Make sure Mutect2 works when both tumor-only and tumor-normal samples…
jfnavarro Mar 9, 2021
f473afe
Merge pull request #356 from MaxUlysse/dev_controlfreec
maxulysse Mar 9, 2021
0b8889d
Make sure Mutect2 works when both tumor-only and tumor-normal samples…
jfnavarro Mar 9, 2021
0e7d5c4
More adjustments to make sure Mutect2 works in tumor-only and tumor-n…
jfnavarro Mar 9, 2021
d68befa
Update main.nf
jfnavarro Mar 9, 2021
7c44773
Merge pull request #354 from jfnavarro/tumoronly
maxulysse Mar 10, 2021
8ff0c14
Template update for nf-core/tools version 1.13
nf-core-bot Mar 18, 2021
86e3c46
Template update for nf-core/tools version 1.13.1
nf-core-bot Mar 19, 2021
ca1d60a
Template update for nf-core/tools version 1.13.2
nf-core-bot Mar 23, 2021
c8721a7
Template update for nf-core/tools version 1.13.3
nf-core-bot Mar 25, 2021
4419e44
feat: remove social preview image to use GitHub OpenGraph
maxulysse Apr 26, 2021
4be42d6
Merge pull request #368 from maxulysse/dev
ewels Apr 26, 2021
3bc9356
feat: add contamination parameter for Control-FREEC
maxulysse May 5, 2021
5cc5c52
Template update for nf-core/tools version 1.14
nf-core-bot May 11, 2021
5e59844
Merge pull request #372 from maxulysse/dev_cf_contamination
maxulysse May 12, 2021
e8c6c6f
Merge remote-tracking branch 'upstream/TEMPLATE' into dev_sync_1.14
maxulysse May 12, 2021
93a3d72
fix: forgot to resolve conflicts here
maxulysse May 12, 2021
70e5f07
fix: schema fixed + remove warnings
maxulysse May 12, 2021
e9f58ee
fix: markdownlint
maxulysse May 12, 2021
a3c6d28
fix: nf-core lint dag error
maxulysse May 13, 2021
7bc1c4a
fix: link to docs
maxulysse May 13, 2021
2e280b6
fix: more lint
maxulysse May 13, 2021
2df52b0
fix: more nf-core lint
maxulysse May 13, 2021
fb4f64e
fix: more nf-core lint
maxulysse May 13, 2021
58f58dc
fix: update files
maxulysse May 13, 2021
af57fab
fix: nf-core lint works
maxulysse May 13, 2021
f7f0b6e
fix: schema
maxulysse May 13, 2021
991dc0f
fix: json schema
maxulysse May 13, 2021
01ed8b4
fix: enum -> list in schema for --tools
maxulysse May 13, 2021
acb7ba8
fix: typo
maxulysse May 13, 2021
d90fa01
fix: typo
maxulysse May 13, 2021
7fe9087
feat: ASCII art is back
maxulysse May 13, 2021
6ca7650
fix: nf-core lint
maxulysse May 13, 2021
b007809
fix: schema
maxulysse May 13, 2021
5e27b2e
Merge pull request #373 from maxulysse/dev_sync_1.14
maxulysse May 13, 2021
546ccd3
feat: nf-core bump-version . 2.7.1
maxulysse May 13, 2021
168b918
feat: manual bump to 2.7.1
maxulysse May 13, 2021
cdcd9cc
fix: cadd_cache is a boolean
maxulysse May 17, 2021
815b0e6
feat: better logo on Github dark Mode
maxulysse May 17, 2021
6ef72f0
Merge pull request #375 from maxulysse/dev_json_fix
maxulysse May 17, 2021
3230b99
Merge remote-tracking branch 'upstream/dev' into dev_2.7.1
maxulysse May 18, 2021
cc483ad
fix: more white
maxulysse May 18, 2021
d7374b0
fix: more white
maxulysse May 18, 2021
672a28b
Merge pull request #376 from maxulysse/dev_logo
maxulysse May 19, 2021
f24eca2
fix: spark issues
maxulysse May 19, 2021
29dae29
fix: cf_ploidy type parameter
maxulysse May 27, 2021
8951221
fix: cf_ploidy type
maxulysse May 27, 2021
6bd689a
Merge pull request #381 from maxulysse/dev_cf_ploidy
maxulysse May 27, 2021
ae806d9
Update nextflow.config
maxulysse May 27, 2021
b3f1fa5
Merge remote-tracking branch 'upstream/dev' into dev_2.7.1
maxulysse May 27, 2021
962e9da
Merge pull request #378 from maxulysse/dev_sparkfix
maxulysse May 27, 2021
9bf1fd5
typo
maxulysse May 27, 2021
0f6bc6d
Merge pull request #382 from maxulysse/dev_cleanup
maxulysse May 27, 2021
ec59f4f
Merge remote-tracking branch 'upstream/dev' into dev_2.7.1
maxulysse May 27, 2021
abbfda0
feat: update CHANGELOG
maxulysse May 27, 2021
29ab231
feat: update CHANGELOG
maxulysse May 27, 2021
d87f60f
Merge pull request #383 from maxulysse/dev_changelog
maxulysse May 27, 2021
4952831
Merge remote-tracking branch 'upstream/dev' into dev_2.7.1
maxulysse May 27, 2021
a7ac118
fix: default value for email is null
maxulysse Jun 1, 2021
789ea5f
feat: update CHANGELOG
maxulysse Jun 1, 2021
7763fe4
fix: null -> empty
maxulysse Jun 1, 2021
a301b0d
Merge pull request #385 from maxulysse/dev_email_json
maxulysse Jun 1, 2021
ba8eed5
Merge remote-tracking branch 'upstream/dev' into dev_2.7.1
maxulysse Jun 1, 2021
412efec
fix: tables for TSV files content
maxulysse Jun 11, 2021
e54a778
feat: update CHANGELOG
maxulysse Jun 11, 2021
6d8d3e4
Merge pull request #387 from maxulysse/dev
maxulysse Jun 11, 2021
3c98945
Merge remote-tracking branch 'upstream/dev' into dev_2.7.1
maxulysse Jun 11, 2021
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20 changes: 10 additions & 10 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ jobs:
environment:
GENOME: GRCh37
SNPEFF_CACHE_VERSION: "75"
SAREK_TAG: 2.7
SAREK_TAG: 2.7.1
steps:
- checkout
- setup_remote_docker
Expand All @@ -20,28 +20,28 @@ jobs:
environment:
GENOME: GRCh38
SNPEFF_CACHE_VERSION: "86"
SAREK_TAG: 2.7
SAREK_TAG: 2.7.1

snpeffgrcm38:
<< : *buildsnpeff
environment:
GENOME: GRCm38
SNPEFF_CACHE_VERSION: "86"
SAREK_TAG: 2.7
SAREK_TAG: 2.7.1

snpeffcanfam3_1:
<< : *buildsnpeff
environment:
GENOME: CanFam3.1
SNPEFF_CACHE_VERSION: "86"
SAREK_TAG: 2.7
SAREK_TAG: 2.7.1

snpeffwbcel235:
<< : *buildsnpeff
environment:
GENOME: WBcel235
SNPEFF_CACHE_VERSION: "86"
SAREK_TAG: 2.7
SAREK_TAG: 2.7.1

vepgrch37: &buildvep
docker:
Expand All @@ -50,7 +50,7 @@ jobs:
GENOME: GRCh37
SPECIES: homo_sapiens
VEP_VERSION: "99"
SAREK_TAG: 2.7
SAREK_TAG: 2.7.1
steps:
- checkout
- setup_remote_docker
Expand All @@ -67,31 +67,31 @@ jobs:
GENOME: GRCh38
SPECIES: homo_sapiens
VEP_VERSION: "99"
SAREK_TAG: 2.7
SAREK_TAG: 2.7.1

vepgrcm38:
<< : *buildvep
environment:
GENOME: GRCm38
SPECIES: mus_musculus
VEP_VERSION: "99"
SAREK_TAG: 2.7
SAREK_TAG: 2.7.1

vepcanfam3_1:
<< : *buildvep
environment:
GENOME: CanFam3.1
SPECIES: canis_familiaris
VEP_VERSION: "99"
SAREK_TAG: 2.7
SAREK_TAG: 2.7.1

vepwbcel235:
<< : *buildvep
environment:
GENOME: WBcel235
SPECIES: caenorhabditis_elegans
VEP_VERSION: "99"
SAREK_TAG: 2.7
SAREK_TAG: 2.7.1

workflows:
version: 2
Expand Down
1 change: 1 addition & 0 deletions .github/.dockstore.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,3 +3,4 @@ version: 1.2
workflows:
- subclass: nfl
primaryDescriptorPath: /nextflow.config
publish: True
4 changes: 2 additions & 2 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ If you wish to contribute a new step, please use the following coding standards:
2. Write the process block (see below).
3. Define the output channel if needed (see below).
4. Add any new flags/options to `nextflow.config` with a default (see below).
5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`)
5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`).
6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
7. Add sanity checks for all relevant parameters.
8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
Expand All @@ -87,7 +87,7 @@ Once there, use `nf-core schema build .` to add to `nextflow_schema.json`.

### Default processes resource requirements

Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.

The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.

Expand Down
9 changes: 4 additions & 5 deletions .github/ISSUE_TEMPLATE/bug_report.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,7 @@ name: Bug report
about: Report something that is broken or incorrect
title: "[BUG]"
labels: bug
assignees: MaxUlysse

assignees: maxulysse
---

<!--
Expand All @@ -21,7 +20,7 @@ Please delete this text and anything that's not relevant from the template below
I have checked the following places for your error:

- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [ ] [nf-core/sarek pipeline documentation](https://nf-co.re/nf-core/sarek/usage)
- [ ] [nf-core/sarek pipeline documentation](https://nf-co.re/sarek/usage)

## Description of the bug

Expand Down Expand Up @@ -58,9 +57,9 @@ Have you provided the following extra information/files:

## Container engine

- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
- Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
- version: <!-- [e.g. 1.0.0] -->
- Image tag: <!-- [e.g. nfcore/sarek:2.6] -->
- Image tag: <!-- [e.g. nfcore/sarek:2.7] -->

## Additional context

Expand Down
3 changes: 1 addition & 2 deletions .github/ISSUE_TEMPLATE/feature_request.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,7 @@ name: Feature request
about: Suggest an idea for the nf-core/sarek pipeline
title: "[FEATURE]"
labels: enhancement
assignees: MaxUlysse

assignees: maxulysse
---

<!--
Expand Down
7 changes: 4 additions & 3 deletions .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
Expand Up @@ -10,14 +10,15 @@ Remember that PRs should be made against the dev branch, unless you're preparing

Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
-->
<!-- markdownlint-disable ul-indent -->

## PR checklist

- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/sarek _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`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
Expand Down
5 changes: 2 additions & 3 deletions .github/markdownlint.yml
Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,8 @@ no-duplicate-header:
siblings_only: true
no-inline-html:
allowed_elements:
- a
- details
- img
- kbd
- p
- kbd
- details
- summary
17 changes: 10 additions & 7 deletions .github/workflows/awsfulltest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,16 @@ on:
types: [completed]
workflow_dispatch:


env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}


jobs:
run-awstest:
name: Run AWS full tests
Expand All @@ -27,13 +37,6 @@ jobs:
# 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:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
run: |
aws batch submit-job \
--region eu-west-1 \
Expand Down
20 changes: 13 additions & 7 deletions .github/workflows/awstest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,16 @@ name: nf-core AWS test
on:
workflow_dispatch:


env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}


jobs:
run-awstest:
name: Run AWS tests
Expand All @@ -20,13 +30,9 @@ jobs:
- name: Install awscli
run: conda install -c conda-forge awscli
- name: Start AWS batch job
env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
# TODO nf-core: You can customise CI pipeline run tests as required
# For example: adding multiple test runs with different parameters
# Remember that you can parallelise this by using strategy.matrix
run: |
aws batch submit-job \
--region eu-west-1 \
Expand Down
16 changes: 13 additions & 3 deletions .github/workflows/branch.yml
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ jobs:
- name: Check PRs
if: github.repository == 'nf-core/sarek'
run: |
{ [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/sarek ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/sarek ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]


# If the above check failed, post a comment on the PR explaining the failure
Expand All @@ -23,14 +23,24 @@ jobs:
uses: mshick/add-pr-comment@v1
with:
message: |
## This PR is against the `master` branch :x:

* Do not close this PR
* Click _Edit_ and change the `base` to `dev`
* This CI test will remain failed until you push a new commit

---

Hi @${{ github.event.pull_request.user.login }},

It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
The `master` branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.

You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!
repo-token: ${{ secrets.GITHUB_TOKEN }}
allow-repeats: false

25 changes: 14 additions & 11 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,9 @@ on:
release:
types: [published]

# Uncomment if we need an edge release of Nextflow again
# env: NXF_EDGE: 1

jobs:
test:
name: Run workflow tests
Expand All @@ -33,13 +36,13 @@ jobs:
environment.yml
- name: Build new docker image
if: env.MATCHED_FILES
run: docker build --no-cache . -t nfcore/sarek:2.7
run: docker build --no-cache . -t nfcore/sarek:2.7.1

- name: Pull docker image
if: ${{ !env.MATCHED_FILES }}
run: |
docker pull nfcore/sarek:dev
docker tag nfcore/sarek:dev nfcore/sarek:2.7
docker tag nfcore/sarek:dev nfcore/sarek:2.7.1

- name: Install Nextflow
env:
Expand Down Expand Up @@ -71,8 +74,8 @@ jobs:
NXF_VER: '20.04.0'
- name: Pull docker image
run: |
docker pull nfcore/sarek:2.7
docker pull nfcore/sarek${{ matrix.tools }}:2.7.${{ matrix.species }}
docker pull nfcore/sarek:2.7.1
docker pull nfcore/sarek${{ matrix.tools }}:2.7.1.${{ matrix.species }}
- name: Run annotation test
run: nextflow run ${GITHUB_WORKSPACE} -profile test_annotation,docker --tools ${{ matrix.tools }}

Expand All @@ -93,7 +96,7 @@ jobs:
# Only check Nextflow pipeline minimum version
NXF_VER: '20.04.0'
- name: Pull docker image
run: docker pull nfcore/sarek:2.7
run: docker pull nfcore/sarek:2.7.1
- name: Get test data
run: git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
- name: Run germline test
Expand Down Expand Up @@ -121,9 +124,9 @@ jobs:
# Only check Nextflow pipeline minimum version
NXF_VER: '20.04.0'
- name: Pull docker image
run: docker pull nfcore/sarek:2.7
run: docker pull nfcore/sarek:2.7.1
- name: Run test for minimal genomes
run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skipQC all --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes
run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skip_qc all --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes

profile:
env:
Expand All @@ -142,7 +145,7 @@ jobs:
# Only check Nextflow pipeline minimum version
NXF_VER: '20.04.0'
- name: Pull docker image
run: docker pull nfcore/sarek:2.7
run: docker pull nfcore/sarek:2.7.1
- name: Run ${{ matrix.profile }} test
run: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker

Expand All @@ -163,7 +166,7 @@ jobs:
# Only check Nextflow pipeline minimum version
NXF_VER: '20.04.0'
- name: Pull docker image
run: docker pull nfcore/sarek:2.7
run: docker pull nfcore/sarek:2.7.1
- name: Run ${{ matrix.profile }} test
run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{ matrix.aligner }}

Expand Down Expand Up @@ -194,6 +197,6 @@ jobs:
# Only check Nextflow pipeline minimum version
NXF_VER: '20.04.0'
- name: Pull docker image
run: docker pull nfcore/sarek:2.7
run: docker pull nfcore/sarek:2.7.1
- name: Run ${{ matrix.tool }} test
run: nextflow run ${GITHUB_WORKSPACE} -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }}
run: nextflow run ${GITHUB_WORKSPACE} -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }}
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