PR for release 1.1.0 #85

KevinMenden · 2021-05-12T05:30:00Z

PR for the release of version 1.1.0.

This release brings a few major and potentially breaking changes.
The main ones:

--input instead of --reads for defining the input data
nfcore_schema.json file for parameters
lib folder with groovy helper functions

fix manifest information

small doc fix

this is related to UMI in the fastq files. Address: #35

A quick patch to fix the handling of --protocol (specifically custom) options when passing off to miRtrace.

Amended documentation around `--protocol` to better reflect that the user can use a custom protocol and provide their own adapter and trimming parameters.

I am updating with the new TEMPLATE and some packages are missing.

update docker with new packages to migrate to new template

update Docker env path

ewels · 2021-05-12T07:20:59Z

So might be nice to look into upgrading some of these packages if possible. And a full size AWS test is always nice.

no default value for single_end parameter (we could also remove that completely as not supported?)

Yes we should remove it completely. Is it just this instance?

smrnaseq/main.nf

Line 184 in 0b54f7b

summary['Data Type'] = params.single_end ? 'Single-End' : 'Paired-End'

KevinMenden · 2021-05-12T07:28:37Z

Great, I'll try updating some of the packages. I probably won't touch the R stuff for now though because that always breaks

Yes I think it was only that ocurrence, fixed it here now:
#86

Will also use that PR to try around with updating the package versions.

cleaned up parameters

added custom into protocol enum

ggabernet

It looks good to me from the pipeline structure perspective, but have no idea on smRNAseq analysis 😄

.github/workflows/awsfulltest.yml

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

removed genome parameters

fix edgeR 1 sample bug

ewels · 2021-06-10T05:04:40Z

Linting shows this:

Config variable not found in main.nf: params.gtf

Don't know if that needs checking before release?

KevinMenden · 2021-06-10T05:18:30Z

Thanks both for having a look! Will see what's going on with that params.gtf later 👍

KevinMenden · 2021-06-10T12:12:45Z

Turns out the gtf param is indeed not used at all, we only have a mirna_gtf param that we use. So I removed gtf and replaced it by mirna_gtf here: #91

github-actions · 2021-06-15T12:44:33Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit b3f3e4d

+| ✅ 213 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  12 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.1.0'
conda_env_yaml - Conda dep outdated: conda-forge::r-base=3.6.3, 4.1.0 available
conda_env_yaml - Conda dep outdated: conda-forge::r-statmod=1.4.32, 1.4.36 available
conda_env_yaml - Conda dep outdated: conda-forge::r-data.table=1.12.4, 1.14.0 available
conda_env_yaml - Conda dep outdated: conda-forge::r-gplots=3.0.1.1, 3.1.1 available
conda_env_yaml - Conda dep outdated: conda-forge::r-r.methodss3=1.7.1, 1.8.1 available
conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.3, 3.9.4 available
conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.1.1, 3.3.4 available
conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=6.0, 8.2 available
conda_env_yaml - Conda dep outdated: bioconda::seqkit=0.16.0, 0.16.1 available
conda_env_yaml - Conda dep outdated: bioconda::bioconductor-edger=3.26.5, 3.34.0 available
conda_env_yaml - Conda dep outdated: bioconda::bioconductor-limma=3.40.2, 3.48.0 available

❔ Tests ignored:

files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: CHANGELOG.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File found: .github/markdownlint.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-smrnaseq_logo.png
files_exist - File found: bin/markdown_to_html.py
files_exist - File found: docs/images/nf-core-smrnaseq_logo.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreSchema.groovy
files_exist - File found: main.nf
files_exist - File found: environment.yml
files_exist - File found: Dockerfile
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable found: process.container
nextflow_config - Config variable (correctly) not found: params.version
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .svg
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config process.container looks correct: nfcore/smrnaseq:1.1.0
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
params_used - Config variable found in main.nf: params.input
params_used - Config variable found in main.nf: params.input_paths
params_used - Config variable found in main.nf: params.outdir
params_used - Config variable found in main.nf: params.protocol
params_used - Config variable found in main.nf: params.genome
params_used - Config variable found in main.nf: params.mirna_gtf
params_used - Config variable found in main.nf: params.bt_indices
params_used - Config variable found in main.nf: params.mirtrace_protocol
params_used - Config variable found in main.nf: params.references_parsed
params_used - Config variable found in main.nf: params.mature
params_used - Config variable found in main.nf: params.hairpin
params_used - Config variable found in main.nf: params.clip_r1
params_used - Config variable found in main.nf: params.three_prime_clip_r1
params_used - Config variable found in main.nf: params.three_prime_adapter
params_used - Config variable found in main.nf: params.min_length
params_used - Config variable found in main.nf: params.skip_qc
params_used - Config variable found in main.nf: params.skip_fastqc
params_used - Config variable found in main.nf: params.skip_multiqc
params_used - Config variable found in main.nf: params.skip_mirdeep
params_used - Config variable found in main.nf: params.save_reference
params_used - Config variable found in main.nf: params.seq_center
params_used - Config variable found in main.nf: params.trim_galore_max_length
params_used - Config variable found in main.nf: params.multiqc_config
params_used - Config variable found in main.nf: params.email
params_used - Config variable found in main.nf: params.email_on_fail
params_used - Config variable found in main.nf: params.max_multiqc_email_size
params_used - Config variable found in main.nf: params.plaintext_email
params_used - Config variable found in main.nf: params.monochrome_logs
params_used - Config variable found in main.nf: params.help
params_used - Config variable found in main.nf: params.tracedir
params_used - Config variable found in main.nf: params.hostnames
params_used - Config variable found in main.nf: params.config_profile_description
params_used - Config variable found in main.nf: params.config_profile_contact
params_used - Config variable found in main.nf: params.config_profile_url
params_used - Config variable found in main.nf: params.publish_dir_mode
params_used - Config variable found in main.nf: params.validate_params
params_used - Config variable found in main.nf: params.max_memory
params_used - Config variable found in main.nf: params.max_cpus
params_used - Config variable found in main.nf: params.max_time
params_used - Config variable found in main.nf: params.bt_index
params_used - Config variable found in main.nf: params.mirtrace_species
params_used - Config variable found in main.nf: params.fasta
files_unchanged - .gitattributes matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.md matches the template
files_unchanged - .github/markdownlint.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-smrnaseq_logo.png matches the template
files_unchanged - bin/markdown_to_html.py matches the template
files_unchanged - docs/images/nf-core-smrnaseq_logo.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .github/workflows/push_dockerhub_dev.yml matches the template
files_unchanged - .github/workflows/push_dockerhub_release.yml matches the template
files_unchanged - assets/multiqc_config.yaml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - CI is building the correct docker image: docker build --no-cache . -t nfcore/smrnaseq:1.1.0
actions_ci - CI is pulling the correct docker image: docker pull nfcore/smrnaseq:dev
actions_ci - CI is tagging docker image correctly: docker tag nfcore/smrnaseq:dev nfcore/smrnaseq:1.1.0
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 20.04.0, Config: 20.04.0
readme - README had a bioconda badge
conda_env_yaml - Conda environment name was correct (nf-core-smrnaseq-1.1.0)
conda_env_yaml - Conda dep had pinned version number: conda-forge::r-base=3.6.3
conda_env_yaml - Conda dep had pinned version number: conda-forge::r-statmod=1.4.32
conda_env_yaml - Conda dep had pinned version number: conda-forge::r-data.table=1.12.4
conda_env_yaml - Conda dep had pinned version number: conda-forge::r-gplots=3.0.1.1
conda_env_yaml - Conda dep had pinned version number: conda-forge::r-r.methodss3=1.7.1
conda_env_yaml - Conda dep had pinned version number: conda-forge::python=3.7.3
conda_env_yaml - Conda dep had pinned version number: conda-forge::markdown=3.1.1
conda_env_yaml - Conda dep had pinned version number: conda-forge::pymdown-extensions=6.0
conda_env_yaml - Conda dep had pinned version number: conda-forge::pygments=2.9.0
conda_env_yaml - Conda package is the latest available: conda-forge::pygments=2.9.0
conda_env_yaml - Conda dep had pinned version number: conda-forge::pigz=2.6
conda_env_yaml - Conda package is the latest available: conda-forge::pigz=2.6
conda_env_yaml - Conda dep had pinned version number: bioconda::fastqc=0.11.9
conda_env_yaml - Conda package is the latest available: bioconda::fastqc=0.11.9
conda_env_yaml - Conda dep had pinned version number: bioconda::trim-galore=0.6.6
conda_env_yaml - Conda package is the latest available: bioconda::trim-galore=0.6.6
conda_env_yaml - Conda dep had pinned version number: bioconda::samtools=1.12
conda_env_yaml - Conda package is the latest available: bioconda::samtools=1.12
conda_env_yaml - Conda dep had pinned version number: bioconda::bowtie=1.3.0
conda_env_yaml - Conda package is the latest available: bioconda::bowtie=1.3.0
conda_env_yaml - Conda dep had pinned version number: bioconda::multiqc=1.10.1
conda_env_yaml - Conda package is the latest available: bioconda::multiqc=1.10.1
conda_env_yaml - Conda dep had pinned version number: bioconda::mirtop=0.4.23
conda_env_yaml - Conda package is the latest available: bioconda::mirtop=0.4.23
conda_env_yaml - Conda dep had pinned version number: bioconda::seqcluster=1.2.7
conda_env_yaml - Conda package is the latest available: bioconda::seqcluster=1.2.7
conda_env_yaml - Conda dep had pinned version number: bioconda::htseq=0.13.5
conda_env_yaml - Conda package is the latest available: bioconda::htseq=0.13.5
conda_env_yaml - Conda dep had pinned version number: bioconda::fastx_toolkit=0.0.14
conda_env_yaml - Conda package is the latest available: bioconda::fastx_toolkit=0.0.14
conda_env_yaml - Conda dep had pinned version number: bioconda::seqkit=0.16.0
conda_env_yaml - Conda dep had pinned version number: bioconda::mirtrace=1.0.1
conda_env_yaml - Conda package is the latest available: bioconda::mirtrace=1.0.1
conda_env_yaml - Conda dep had pinned version number: bioconda::bioconductor-edger=3.26.5
conda_env_yaml - Conda dep had pinned version number: bioconda::bioconductor-limma=3.40.2
conda_env_yaml - Conda dep had pinned version number: bioconda::mirdeep2=2.0.1.2
conda_env_yaml - Conda package is the latest available: bioconda::mirdeep2=2.0.1.2
conda_dockerfile - Found all expected strings in Dockerfile file
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (55 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files

Run details

nf-core/tools version 1.14
Run at 2021-06-15 12:11:38

ewels and others added 30 commits July 13, 2018 14:43

Added basic shell of documentation

4c97d97

fix authors

b6f1177

fix authors

b21a7da

fix title

dcb5e85

fix manifest

fff18be

fix markdown lint

8bf75ac

Merge pull request #18 from lpantano/TEMPLATE

03d3d90

fix manifest information

Merge branch 'dev' of github.com:nf-core/smrnaseq

ad28fe4

small doc fix

1a99cd6

Merge pull request #34 from KevinMenden/master

7a139ec

small doc fix

make sure one file is used in collapse step

7b0bfd8

this is related to UMI in the fastq files. Address: #35

add changelog updates and new version

4969809

add social preview image

2b3e647

update CHANGELOG

4e823c9

remove links to non-existing 1.0 releases

acf380a

Template update for nf-core/tools version 1.9

3a71bc9

custom protocol implementation

949b5c4

A quick patch to fix the handling of --protocol (specifically custom) options when passing off to miRtrace.

improved --protocol documentation

675b45c

Amended documentation around `--protocol` to better reflect that the user can use a custom protocol and provide their own adapter and trimming parameters.

update docker with new packages to migrate to new template

2160233

I am updating with the new TEMPLATE and some packages are missing.

update changelog

a03cd1f

Merge pull request #45 from nf-core/lpantano-patch-docker

cf1061d

update docker with new packages to migrate to new template

Merge branch 'TEMPLATE' into dev

d71e786

update Docker env path

7f8bc88

get docker working

4f131ff

Merge branch 'lpantano-patch-docker' into dev

d894348

Update changelog

6bbfe68

Merge branch 'lpantano-patch-docker' into dev

07a1a8c

Merge pull request #46 from nf-core/lpantano-patch-docker

22961b4

update Docker env path

update change log

07611c3

fix markdown linting errors

c510dc8

changelog

f51bb96

KevinMenden and others added 4 commits May 12, 2021 09:36

fixed bug; updated some versions

b308737

Merge pull request #86 from KevinMenden/dev

f7c91d2

cleaned up parameters

added custom into protocol enum

f6e843c

Merge pull request #87 from KevinMenden/dev

f1b8075

added custom into protocol enum

ggabernet approved these changes May 12, 2021

View reviewed changes

.github/workflows/awsfulltest.yml Outdated Show resolved Hide resolved

KevinMenden and others added 12 commits May 17, 2021 07:09

Update .github/workflows/awsfulltest.yml

215835c

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

removed genome parameters

968c7b0

adjusted bowtie_indices projcess

93ef876

use bug-fixed NfcoreSchema.groovy file

eea3dd2

Update nextflow.config

ad2d3de

Merge pull request #89 from KevinMenden/dev

2acc845

removed genome parameters

fixed nfcoreschema bug

3735334

Merge branch 'dev' of https://github.com/KevinMenden/smrnaseq into dev

666e02a

fixed edgeR mirbase bug (1 sample)

810f5ed

Merge branch 'dev' of https://github.com/nf-core/smrnaseq into dev

5af9fa6

additional check in edgeR script

3d52a6b

Merge pull request #90 from KevinMenden/dev

3b27536

fix edgeR 1 sample bug

lpantano approved these changes Jun 9, 2021

View reviewed changes

KevinMenden added 2 commits June 10, 2021 14:09

replace gtf with mirna_gtf

06413d0

remove gtf from schema

179df50

ewels and others added 2 commits June 10, 2021 15:28

Merge pull request #91 from KevinMenden/dev

90d366c

update release date

b3f3e4d

KevinMenden merged commit 03333bf into master Jun 15, 2021

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PR for release 1.1.0 #85

PR for release 1.1.0 #85

KevinMenden commented May 12, 2021

ewels commented May 12, 2021

KevinMenden commented May 12, 2021

ggabernet left a comment

ewels commented Jun 10, 2021

KevinMenden commented Jun 10, 2021

KevinMenden commented Jun 10, 2021

github-actions bot commented Jun 15, 2021

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

PR for release 1.1.0 #85

PR for release 1.1.0 #85

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KevinMenden commented May 12, 2021

ewels commented May 12, 2021

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ewels commented Jun 10, 2021

KevinMenden commented Jun 10, 2021

KevinMenden commented Jun 10, 2021

github-actions bot commented Jun 15, 2021

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

`nf-core lint` overall result: Passed ✅ ⚠️