Dev -> Master for 2.1 release #203

drpatelh · 2021-06-10T22:16:08Z

No description provided.

Bump version to 2.1dev

Bump nextclade and pangolin version

github-actions · 2021-06-10T22:17:16Z

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

Posted for pipeline commit 9fd5ef2

+| ✅ 115 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗  82 tests had warnings |!

❗ Test warnings:

files_exist - File not found: environment.yml
files_exist - File not found: Dockerfile
nextflow_config - Config variable not found: process.container
nextflow_config - Config manifest.version should end in dev: '2.1'
params_used - Config variable not found in main.nf: params.input
params_used - Config variable not found in main.nf: params.genome
params_used - Config variable not found in main.nf: params.primer_fasta
params_used - Config variable not found in main.nf: params.primer_left_suffix
params_used - Config variable not found in main.nf: params.primer_right_suffix
params_used - Config variable not found in main.nf: params.save_reference
params_used - Config variable not found in main.nf: params.fastq_dir
params_used - Config variable not found in main.nf: params.fast5_dir
params_used - Config variable not found in main.nf: params.sequencing_summary
params_used - Config variable not found in main.nf: params.min_barcode_reads
params_used - Config variable not found in main.nf: params.min_guppyplex_reads
params_used - Config variable not found in main.nf: params.artic_minion_caller
params_used - Config variable not found in main.nf: params.artic_minion_aligner
params_used - Config variable not found in main.nf: params.artic_minion_medaka_model
params_used - Config variable not found in main.nf: params.skip_pycoqc
params_used - Config variable not found in main.nf: params.skip_nanoplot
params_used - Config variable not found in main.nf: params.asciigenome_read_depth
params_used - Config variable not found in main.nf: params.asciigenome_window_size
params_used - Config variable not found in main.nf: params.multiqc_title
params_used - Config variable not found in main.nf: params.multiqc_config
params_used - Config variable not found in main.nf: params.max_multiqc_email_size
params_used - Config variable not found in main.nf: params.skip_mosdepth
params_used - Config variable not found in main.nf: params.skip_pangolin
params_used - Config variable not found in main.nf: params.skip_nextclade
params_used - Config variable not found in main.nf: params.skip_asciigenome
params_used - Config variable not found in main.nf: params.skip_variants_quast
params_used - Config variable not found in main.nf: params.skip_multiqc
params_used - Config variable not found in main.nf: params.kraken2_db
params_used - Config variable not found in main.nf: params.kraken2_db_name
params_used - Config variable not found in main.nf: params.kraken2_variants_host_filter
params_used - Config variable not found in main.nf: params.kraken2_assembly_host_filter
params_used - Config variable not found in main.nf: params.save_trimmed_fail
params_used - Config variable not found in main.nf: params.skip_fastqc
params_used - Config variable not found in main.nf: params.skip_kraken2
params_used - Config variable not found in main.nf: params.skip_fastp
params_used - Config variable not found in main.nf: params.skip_cutadapt
params_used - Config variable not found in main.nf: params.callers
params_used - Config variable not found in main.nf: params.min_mapped_reads
params_used - Config variable not found in main.nf: params.ivar_trim_noprimer
params_used - Config variable not found in main.nf: params.ivar_trim_offset
params_used - Config variable not found in main.nf: params.filter_duplicates
params_used - Config variable not found in main.nf: params.save_unaligned
params_used - Config variable not found in main.nf: params.save_mpileup
params_used - Config variable not found in main.nf: params.skip_ivar_trim
params_used - Config variable not found in main.nf: params.skip_markduplicates
params_used - Config variable not found in main.nf: params.skip_picard_metrics
params_used - Config variable not found in main.nf: params.skip_snpeff
params_used - Config variable not found in main.nf: params.skip_consensus
params_used - Config variable not found in main.nf: params.skip_variants
params_used - Config variable not found in main.nf: params.assemblers
params_used - Config variable not found in main.nf: params.spades_mode
params_used - Config variable not found in main.nf: params.spades_hmm
params_used - Config variable not found in main.nf: params.blast_db
params_used - Config variable not found in main.nf: params.skip_bandage
params_used - Config variable not found in main.nf: params.skip_blast
params_used - Config variable not found in main.nf: params.skip_abacas
params_used - Config variable not found in main.nf: params.skip_plasmidid
params_used - Config variable not found in main.nf: params.skip_assembly_quast
params_used - Config variable not found in main.nf: params.skip_assembly
params_used - Config variable not found in main.nf: params.outdir
params_used - Config variable not found in main.nf: params.tracedir
params_used - Config variable not found in main.nf: params.publish_dir_mode
params_used - Config variable not found in main.nf: params.email
params_used - Config variable not found in main.nf: params.email_on_fail
params_used - Config variable not found in main.nf: params.plaintext_email
params_used - Config variable not found in main.nf: params.monochrome_logs
params_used - Config variable not found in main.nf: params.help
params_used - Config variable not found in main.nf: params.enable_conda
params_used - Config variable not found in main.nf: params.singularity_pull_docker_container
params_used - Config variable not found in main.nf: params.validate_params
params_used - Config variable not found in main.nf: params.hostnames
params_used - Config variable not found in main.nf: params.config_profile_description
params_used - Config variable not found in main.nf: params.config_profile_contact
params_used - Config variable not found in main.nf: params.config_profile_url
params_used - Config variable not found in main.nf: params.max_memory
params_used - Config variable not found in main.nf: params.max_cpus
params_used - Config variable not found in main.nf: params.max_time
readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

files_exist - File is ignored: bin/markdown_to_html.py
files_exist - File is ignored: .github/markdownlint.yml
files_unchanged - File ignored due to lint config: .github/markdownlint.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: bin/markdown_to_html.py
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
files_unchanged - File does not exist: .github/workflows/push_dockerhub_dev.yml
files_unchanged - File does not exist: .github/workflows/push_dockerhub_release.yml
files_unchanged - File does not exist: assets/multiqc_config.yaml
actions_awsfulltest - actions_awsfulltest
conda_env_yaml - No environment.yml file found - skipping conda_env_yaml test
conda_dockerfile - No environment.yml / Dockerfile file found - skipping conda_dockerfile test

✅ 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/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-viralrecon_logo.png
files_exist - File found: docs/images/nf-core-viralrecon_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: 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 (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 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.platform
params_used - Config variable found in main.nf: params.protocol
params_used - Config variable found in main.nf: params.primer_set
params_used - Config variable found in main.nf: params.primer_set_version
params_used - Config variable found in main.nf: params.artic_scheme
params_used - Config variable found in main.nf: params.fasta
params_used - Config variable found in main.nf: params.gff
params_used - Config variable found in main.nf: params.bowtie2_index
params_used - Config variable found in main.nf: params.primer_bed
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/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/nf-core-viralrecon_logo.png matches the template
files_unchanged - docs/images/nf-core-viralrecon_logo.png matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - .gitignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (266 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: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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 2021-06-14 14:51:04

JoseEspinosa

Looks awesome as always! 🎸
Just made a small suggestion!

JoseEspinosa · 2021-06-11T08:15:19Z

CHANGELOG.md

+
+* Removed workflow to download data from public databases in favour of using [nf-core/fetchngs](https://nf-co.re/fetchngs)
+* Added Pangolin VOC scorpio calls to default variant calling summary metrics
+* Dashes in sample names will be converted to underscores to avoid issues when creating the summary metrics via QUAST


Suggested change

* Dashes in sample names will be converted to underscores to avoid issues when creating the summary metrics via QUAST

Dashes and spaces in sample names will be converted to underscores to avoid issues when creating the summary metrics via QUAST

Fixed aaec38e 🦅 👀

heuermh

LGTM!

JoseEspinosa · 2021-06-11T21:29:30Z

Sorry, I closed it by mistake on the phone app... 🤦 reopened 1 sec after but...

Add amplicon heatmap to MultiQC

Fix snpEff OutofMemory errors

…pore

…mina

Add Nextclade clade info to summary metrics and MultiQC report

drpatelh and others added 30 commits May 13, 2021 17:17

Update CHANGELOG

d1c468c

Merge pull request #195 from drpatelh/updates

268a07b

Bump version to 2.1dev

Remove test_sra CI workflow

a73f1d4

Remove docs for fetching public data

bb783db

Remove section for fetching public data

a3a825e

Add section about Nanopore input format to usage docs

eb26d8b

Fix tyop

ee8a6f5

Delete SRA download specific files

cb0b41d

Add camelCase bug fix for Schema

909bd6d

Remove SRA download workflow call

5cb43a1

Remove SRA download specific parameters

70095e4

Remove schema for public_data_ids

47fec28

Add links to new docs in README

49fd0e5

Add description for SWIFT protocol to usage docs

efede86

Fix tests

54224ad

Auto-replace dashes with underscores in sample names

012ae50

Add docs about moving SRA download workflow to fetchngs

75da4af

Fix tyop

d4c5d91

Add usage docs about updating container version

e4c8817

fix Tyops

7d5812e

Update nextclade version to 0.14.4

5cf9e29

Update pangolin version to 2.4.2

05e0b53

Merge pull request #200 from JoseEspinosa/bump_nextclade_pangolin

dd9b742

Bump nextclade and pangolin version

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

9bde3ca

Update CHANGELOG

5165fe3

Bump pipeline version to 2.1

80f408d

Add warning to MultiQC if 0 reads after adapter trimming

fac02c2

EClint fix indents in yaml

691865c

Finesse code to report samples with no reads after trimming

d75af8b

Create empty channel if skipping trimming

d0da25e

drpatelh added 5 commits June 10, 2021 23:10

Adjust channels to add sizes file

c74b337

Adjust channels to add sizes file

91b540d

Use sizes file when calling ASCIIGenome

c0336b4

Use sizes file when calling ASCIIGenome

58a67c4

Add local module to get chromosome sizes

ec5dce5

JoseEspinosa self-requested a review June 11, 2021 08:11

JoseEspinosa approved these changes Jun 11, 2021

View reviewed changes

drpatelh added 2 commits June 11, 2021 17:27

Add Pangolin results to MultiQC report

5c131ac

Update CHANGELOG

aaec38e

heuermh approved these changes Jun 11, 2021

View reviewed changes

JoseEspinosa closed this Jun 11, 2021

JoseEspinosa reopened this Jun 11, 2021

drpatelh and others added 15 commits June 13, 2021 09:48

Add QUAST metrics to MultiQC report

0820b17

Merge pull request #202 from drpatelh/updates

96ab384

Add amplicon heatmap to MultiQC

Fix snpEff OutofMemory errors

2496da0

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

405a06f

Remove cache statement used for testing

9c2ca29

Rename module to create custom MultiQC content

cfbd52a

Merge pull request #205 from drpatelh/updates

42902e3

Fix snpEff OutofMemory errors

Add Nextclade clade info to summary metrics and MultiQC report - nano…

2f39108

…pore

Fix merge conflicts

c038cd4

Update CHANGELOG

0681d0d

Add Nextclade clade info to summary metrics and MultiQC report - illu…

af854a4

…mina

Update CHANGELOG

513146b

Add correct channel name after erroneous merge conflict fix

cbfc3d5

Remove braces in docs

70cd8db

Merge pull request #206 from drpatelh/nextclade

9fd5ef2

Add Nextclade clade info to summary metrics and MultiQC report

drpatelh merged commit f017132 into master Jun 15, 2021

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Dev -> Master for 2.1 release #203

Dev -> Master for 2.1 release #203

drpatelh commented Jun 10, 2021

github-actions bot commented Jun 10, 2021 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

JoseEspinosa left a comment

JoseEspinosa Jun 11, 2021

drpatelh Jun 11, 2021

heuermh left a comment

JoseEspinosa commented Jun 11, 2021

	* Dashes in sample names will be converted to underscores to avoid issues when creating the summary metrics via QUAST
	Dashes and spaces in sample names will be converted to underscores to avoid issues when creating the summary metrics via QUAST

Dev -> Master for 2.1 release #203

Dev -> Master for 2.1 release #203

Conversation

drpatelh commented Jun 10, 2021

github-actions bot commented Jun 10, 2021 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

JoseEspinosa left a comment

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JoseEspinosa Jun 11, 2021

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drpatelh Jun 11, 2021

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heuermh left a comment

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JoseEspinosa commented Jun 11, 2021

github-actions bot commented Jun 10, 2021 •

edited

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