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Fixed TSV input documentation #914

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Merged
apeltzer merged 2 commits into from
Sep 5, 2022
Merged

Fixed TSV input documentation #914

apeltzer merged 2 commits into from
Sep 5, 2022

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@aidaanva
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@aidaanva aidaanva commented Aug 25, 2022 •
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Removed the second fastq in the SE data in the example of the TSV input, since this should be NA for single-end data

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/eager/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/eager branch on the 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.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@aidaanva aidaanva requested a review from jfy133 August 25, 2022 12:00
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github-actions bot commented Aug 25, 2022

This PR is against the master branch ❌

  • Do not close this PR
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  • This CI test will remain failed until you push a new commit

Hi @aidaanva,

It looks like this pull-request is has been made against the nf-core/eager 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 nf-core/eager 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.
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@aidaanva aidaanva changed the base branch from master to dev August 25, 2022 12:00
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github-actions bot commented Aug 25, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8b42000

+| ✅ 388 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  30 tests had warnings |!
Details

❗ Test warnings:

  • params_used - Config variable not found in main.nf: params.input_paths
  • params_used - Config variable not found in main.nf: params.enable_conda
  • conda_env_yaml - Conda dep outdated: conda-forge::python=3.9.4, 3.10.6 available
  • conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.3.4, 3.4.1 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=8.2, 9.5 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.9.0, 2.13.0 available
  • conda_env_yaml - Conda dep outdated: conda-forge::openjdk=8.0.144, 17.0.3 available
  • conda_env_yaml - Conda dep outdated: bioconda::adapterremoval=2.3.2, 2.3.3 available
  • conda_env_yaml - Conda dep outdated: bioconda::picard=2.26.0, 2.27.4 available
  • conda_env_yaml - Conda dep outdated: bioconda::samtools=1.12, 1.15.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::angsd=0.935, 0.939 available
  • conda_env_yaml - Conda dep outdated: bioconda::gatk4=4.2.0.0, 4.2.6.0 available
  • conda_env_yaml - Conda dep outdated: bioconda::gatk=3.5, 3.8 available
  • conda_env_yaml - Conda dep outdated: bioconda::damageprofiler=0.4.9, 1.1 available
  • conda_env_yaml - Conda dep outdated: conda-forge::libiconv=1.16, 1.17 available
  • conda_env_yaml - Conda dep outdated: bioconda::fastp=0.20.1, 0.23.2 available
  • conda_env_yaml - Conda dep outdated: bioconda::pysam=0.16.0, 0.19.1 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pandas=1.2.4, 1.4.3 available
  • conda_env_yaml - Conda dep outdated: bioconda::freebayes=1.3.5, 1.3.6 available
  • conda_env_yaml - Conda dep outdated: conda-forge::xopen=1.1.0, 1.6.0 available
  • conda_env_yaml - Conda dep outdated: bioconda::bowtie2=2.4.4, 2.4.5 available
  • conda_env_yaml - Conda dep outdated: bioconda::eigenstratdatabasetools=1.0.2, 1.1.0 available
  • conda_env_yaml - Conda dep outdated: bioconda::bbmap=38.92, 38.98 available
  • conda_env_yaml - Conda dep outdated: bioconda::bcftools=1.12, 1.15.1 available
  • schema_description - No description provided in schema for parameter: skip_fastqc
  • schema_description - No description provided in schema for parameter: skip_adapterremoval
  • schema_description - No description provided in schema for parameter: skip_preseq
  • schema_description - No description provided in schema for parameter: skip_deduplication
  • schema_description - No description provided in schema for parameter: skip_damage_calculation
  • schema_description - No description provided in schema for parameter: skip_qualimap

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ 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-eager_logo.png
  • files_exist - File found: bin/markdown_to_html.py
  • files_exist - File found: docs/images/nf-core-eager_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/eager:dev
  • nextflow_config - Config manifest.version ends in dev: '2.4.5dev'
  • 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.genome
  • params_used - Config variable found in main.nf: params.input
  • params_used - Config variable found in main.nf: params.single_end
  • params_used - Config variable found in main.nf: params.outdir
  • params_used - Config variable found in main.nf: params.publish_dir_mode
  • params_used - Config variable found in main.nf: params.awsqueue
  • params_used - Config variable found in main.nf: params.awsregion
  • params_used - Config variable found in main.nf: params.awscli
  • params_used - Config variable found in main.nf: params.validate_params
  • params_used - Config variable found in main.nf: params.udg_type
  • params_used - Config variable found in main.nf: params.single_stranded
  • params_used - Config variable found in main.nf: params.colour_chemistry
  • params_used - Config variable found in main.nf: params.bam
  • params_used - Config variable found in main.nf: params.snpcapture_bed
  • params_used - Config variable found in main.nf: params.run_convertinputbam
  • params_used - Config variable found in main.nf: params.fasta
  • params_used - Config variable found in main.nf: params.bwa_index
  • params_used - Config variable found in main.nf: params.bt2_index
  • params_used - Config variable found in main.nf: params.fasta_index
  • params_used - Config variable found in main.nf: params.seq_dict
  • params_used - Config variable found in main.nf: params.large_ref
  • params_used - Config variable found in main.nf: params.save_reference
  • params_used - Config variable found in main.nf: params.genomes
  • params_used - Config variable found in main.nf: params.skip_fastqc
  • params_used - Config variable found in main.nf: params.skip_adapterremoval
  • params_used - Config variable found in main.nf: params.skip_preseq
  • params_used - Config variable found in main.nf: params.skip_deduplication
  • params_used - Config variable found in main.nf: params.skip_damage_calculation
  • params_used - Config variable found in main.nf: params.skip_qualimap
  • params_used - Config variable found in main.nf: params.complexity_filter_poly_g
  • params_used - Config variable found in main.nf: params.complexity_filter_poly_g_min
  • params_used - Config variable found in main.nf: params.clip_forward_adaptor
  • params_used - Config variable found in main.nf: params.clip_reverse_adaptor
  • params_used - Config variable found in main.nf: params.clip_adapters_list
  • params_used - Config variable found in main.nf: params.clip_readlength
  • params_used - Config variable found in main.nf: params.clip_min_read_quality
  • params_used - Config variable found in main.nf: params.min_adap_overlap
  • params_used - Config variable found in main.nf: params.skip_collapse
  • params_used - Config variable found in main.nf: params.skip_trim
  • params_used - Config variable found in main.nf: params.preserve5p
  • params_used - Config variable found in main.nf: params.mergedonly
  • params_used - Config variable found in main.nf: params.qualitymax
  • params_used - Config variable found in main.nf: params.run_post_ar_trimming
  • params_used - Config variable found in main.nf: params.post_ar_trim_front
  • params_used - Config variable found in main.nf: params.post_ar_trim_tail
  • params_used - Config variable found in main.nf: params.post_ar_trim_front2
  • params_used - Config variable found in main.nf: params.post_ar_trim_tail2
  • params_used - Config variable found in main.nf: params.mapper
  • params_used - Config variable found in main.nf: params.bwaalnn
  • params_used - Config variable found in main.nf: params.bwaalnk
  • params_used - Config variable found in main.nf: params.bwaalnl
  • params_used - Config variable found in main.nf: params.bwaalno
  • params_used - Config variable found in main.nf: params.circularextension
  • params_used - Config variable found in main.nf: params.circulartarget
  • params_used - Config variable found in main.nf: params.circularfilter
  • params_used - Config variable found in main.nf: params.bt2_alignmode
  • params_used - Config variable found in main.nf: params.bt2_sensitivity
  • params_used - Config variable found in main.nf: params.bt2n
  • params_used - Config variable found in main.nf: params.bt2l
  • params_used - Config variable found in main.nf: params.bt2_trim5
  • params_used - Config variable found in main.nf: params.bt2_trim3
  • params_used - Config variable found in main.nf: params.bt2_maxins
  • params_used - Config variable found in main.nf: params.hostremoval_input_fastq
  • params_used - Config variable found in main.nf: params.hostremoval_mode
  • params_used - Config variable found in main.nf: params.run_bam_filtering
  • params_used - Config variable found in main.nf: params.bam_mapping_quality_threshold
  • params_used - Config variable found in main.nf: params.bam_filter_minreadlength
  • params_used - Config variable found in main.nf: params.bam_unmapped_type
  • params_used - Config variable found in main.nf: params.dedupper
  • params_used - Config variable found in main.nf: params.dedup_all_merged
  • params_used - Config variable found in main.nf: params.preseq_step_size
  • params_used - Config variable found in main.nf: params.preseq_mode
  • params_used - Config variable found in main.nf: params.preseq_bootstrap
  • params_used - Config variable found in main.nf: params.preseq_maxextrap
  • params_used - Config variable found in main.nf: params.preseq_cval
  • params_used - Config variable found in main.nf: params.preseq_terms
  • params_used - Config variable found in main.nf: params.damageprofiler_length
  • params_used - Config variable found in main.nf: params.damageprofiler_threshold
  • params_used - Config variable found in main.nf: params.damageprofiler_yaxis
  • params_used - Config variable found in main.nf: params.run_pmdtools
  • params_used - Config variable found in main.nf: params.pmdtools_range
  • params_used - Config variable found in main.nf: params.pmdtools_threshold
  • params_used - Config variable found in main.nf: params.pmdtools_reference_mask
  • params_used - Config variable found in main.nf: params.pmdtools_max_reads
  • params_used - Config variable found in main.nf: params.pmdtools_platypus
  • params_used - Config variable found in main.nf: params.run_mapdamage_rescaling
  • params_used - Config variable found in main.nf: params.rescale_length_5p
  • params_used - Config variable found in main.nf: params.rescale_length_3p
  • params_used - Config variable found in main.nf: params.run_bedtools_coverage
  • params_used - Config variable found in main.nf: params.anno_file
  • params_used - Config variable found in main.nf: params.run_trim_bam
  • params_used - Config variable found in main.nf: params.bamutils_clip_double_stranded_half_udg_left
  • params_used - Config variable found in main.nf: params.bamutils_clip_double_stranded_half_udg_right
  • params_used - Config variable found in main.nf: params.bamutils_clip_double_stranded_none_udg_left
  • params_used - Config variable found in main.nf: params.bamutils_clip_double_stranded_none_udg_right
  • params_used - Config variable found in main.nf: params.bamutils_clip_single_stranded_half_udg_left
  • params_used - Config variable found in main.nf: params.bamutils_clip_single_stranded_half_udg_right
  • params_used - Config variable found in main.nf: params.bamutils_clip_single_stranded_none_udg_left
  • params_used - Config variable found in main.nf: params.bamutils_clip_single_stranded_none_udg_right
  • params_used - Config variable found in main.nf: params.bamutils_softclip
  • params_used - Config variable found in main.nf: params.run_genotyping
  • params_used - Config variable found in main.nf: params.genotyping_tool
  • params_used - Config variable found in main.nf: params.genotyping_source
  • params_used - Config variable found in main.nf: params.gatk_call_conf
  • params_used - Config variable found in main.nf: params.gatk_ploidy
  • params_used - Config variable found in main.nf: params.gatk_downsample
  • params_used - Config variable found in main.nf: params.gatk_dbsnp
  • params_used - Config variable found in main.nf: params.gatk_hc_out_mode
  • params_used - Config variable found in main.nf: params.gatk_hc_emitrefconf
  • params_used - Config variable found in main.nf: params.gatk_ug_genotype_model
  • params_used - Config variable found in main.nf: params.gatk_ug_out_mode
  • params_used - Config variable found in main.nf: params.gatk_ug_keep_realign_bam
  • params_used - Config variable found in main.nf: params.gatk_ug_defaultbasequalities
  • params_used - Config variable found in main.nf: params.freebayes_C
  • params_used - Config variable found in main.nf: params.freebayes_g
  • params_used - Config variable found in main.nf: params.freebayes_p
  • params_used - Config variable found in main.nf: params.pileupcaller_snpfile
  • params_used - Config variable found in main.nf: params.pileupcaller_bedfile
  • params_used - Config variable found in main.nf: params.pileupcaller_method
  • params_used - Config variable found in main.nf: params.pileupcaller_transitions_mode
  • params_used - Config variable found in main.nf: params.pileupcaller_min_map_quality
  • params_used - Config variable found in main.nf: params.pileupcaller_min_base_quality
  • params_used - Config variable found in main.nf: params.angsd_glmodel
  • params_used - Config variable found in main.nf: params.angsd_glformat
  • params_used - Config variable found in main.nf: params.angsd_createfasta
  • params_used - Config variable found in main.nf: params.angsd_fastamethod
  • params_used - Config variable found in main.nf: params.run_bcftools_stats
  • params_used - Config variable found in main.nf: params.run_vcf2genome
  • params_used - Config variable found in main.nf: params.vcf2genome_outfile
  • params_used - Config variable found in main.nf: params.vcf2genome_header
  • params_used - Config variable found in main.nf: params.vcf2genome_minc
  • params_used - Config variable found in main.nf: params.vcf2genome_minq
  • params_used - Config variable found in main.nf: params.vcf2genome_minfreq
  • params_used - Config variable found in main.nf: params.run_multivcfanalyzer
  • params_used - Config variable found in main.nf: params.write_allele_frequencies
  • params_used - Config variable found in main.nf: params.min_genotype_quality
  • params_used - Config variable found in main.nf: params.min_base_coverage
  • params_used - Config variable found in main.nf: params.min_allele_freq_hom
  • params_used - Config variable found in main.nf: params.min_allele_freq_het
  • params_used - Config variable found in main.nf: params.additional_vcf_files
  • params_used - Config variable found in main.nf: params.reference_gff_annotations
  • params_used - Config variable found in main.nf: params.reference_gff_exclude
  • params_used - Config variable found in main.nf: params.snp_eff_results
  • params_used - Config variable found in main.nf: params.run_mtnucratio
  • params_used - Config variable found in main.nf: params.mtnucratio_header
  • params_used - Config variable found in main.nf: params.run_sexdeterrmine
  • params_used - Config variable found in main.nf: params.sexdeterrmine_bedfile
  • params_used - Config variable found in main.nf: params.run_nuclear_contamination
  • params_used - Config variable found in main.nf: params.contamination_chrom_name
  • params_used - Config variable found in main.nf: params.run_metagenomic_screening
  • params_used - Config variable found in main.nf: params.metagenomic_complexity_filter
  • params_used - Config variable found in main.nf: params.metagenomic_complexity_entropy
  • params_used - Config variable found in main.nf: params.metagenomic_tool
  • params_used - Config variable found in main.nf: params.database
  • params_used - Config variable found in main.nf: params.metagenomic_min_support_reads
  • params_used - Config variable found in main.nf: params.percent_identity
  • params_used - Config variable found in main.nf: params.malt_mode
  • params_used - Config variable found in main.nf: params.malt_alignment_mode
  • params_used - Config variable found in main.nf: params.malt_top_percent
  • params_used - Config variable found in main.nf: params.malt_min_support_mode
  • params_used - Config variable found in main.nf: params.malt_min_support_percent
  • params_used - Config variable found in main.nf: params.malt_max_queries
  • params_used - Config variable found in main.nf: params.malt_memory_mode
  • params_used - Config variable found in main.nf: params.malt_sam_output
  • params_used - Config variable found in main.nf: params.run_maltextract
  • params_used - Config variable found in main.nf: params.maltextract_taxon_list
  • params_used - Config variable found in main.nf: params.maltextract_ncbifiles
  • params_used - Config variable found in main.nf: params.maltextract_filter
  • params_used - Config variable found in main.nf: params.maltextract_toppercent
  • params_used - Config variable found in main.nf: params.maltextract_destackingoff
  • params_used - Config variable found in main.nf: params.maltextract_downsamplingoff
  • params_used - Config variable found in main.nf: params.maltextract_duplicateremovaloff
  • params_used - Config variable found in main.nf: params.maltextract_matches
  • params_used - Config variable found in main.nf: params.maltextract_megansummary
  • params_used - Config variable found in main.nf: params.maltextract_percentidentity
  • params_used - Config variable found in main.nf: params.maltextract_topalignment
  • 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.max_memory
  • params_used - Config variable found in main.nf: params.max_cpus
  • params_used - Config variable found in main.nf: params.max_time
  • 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/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 - 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-eager_logo.png matches the template
  • files_unchanged - bin/markdown_to_html.py matches the template
  • files_unchanged - docs/images/nf-core-eager_logo.png matches the template
  • files_unchanged - lib/nfcore_external_java_deps.jar matches the template
  • files_unchanged - lib/NfcoreSchema.groovy 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
  • 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/eager:dev
  • actions_ci - CI is pulling the correct docker image: docker pull nfcore/eager:dev
  • actions_ci - CI is tagging docker image correctly: docker tag nfcore/eager:dev nfcore/eager:dev
  • 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: 20.07.1, Config: 20.07.1
  • readme - README had a bioconda badge
  • conda_env_yaml - Conda environment name was correct (nf-core-eager-2.4.5dev)
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::python=3.9.4
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::markdown=3.3.4
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::pymdown-extensions=8.2
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::pygments=2.9.0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::rename=1.601
  • conda_env_yaml - Conda package is the latest available: bioconda::rename=1.601
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::openjdk=8.0.144
  • 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::adapterremoval=2.3.2
  • conda_env_yaml - Conda dep had pinned version number: bioconda::adapterremovalfixprefix=0.0.5
  • conda_env_yaml - Conda package is the latest available: bioconda::adapterremovalfixprefix=0.0.5
  • conda_env_yaml - Conda dep had pinned version number: bioconda::bwa=0.7.17
  • conda_env_yaml - Conda package is the latest available: bioconda::bwa=0.7.17
  • conda_env_yaml - Conda dep had pinned version number: bioconda::picard=2.26.0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::samtools=1.12
  • conda_env_yaml - Conda dep had pinned version number: bioconda::dedup=0.12.8
  • conda_env_yaml - Conda package is the latest available: bioconda::dedup=0.12.8
  • conda_env_yaml - Conda dep had pinned version number: bioconda::angsd=0.935
  • conda_env_yaml - Conda dep had pinned version number: bioconda::circularmapper=1.93.5
  • conda_env_yaml - Conda package is the latest available: bioconda::circularmapper=1.93.5
  • conda_env_yaml - Conda dep had pinned version number: bioconda::gatk4=4.2.0.0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::gatk=3.5
  • conda_env_yaml - Conda dep had pinned version number: bioconda::qualimap=2.2.2d
  • conda_env_yaml - Conda package is the latest available: bioconda::qualimap=2.2.2d
  • conda_env_yaml - Conda dep had pinned version number: bioconda::vcf2genome=0.91
  • conda_env_yaml - Conda package is the latest available: bioconda::vcf2genome=0.91
  • conda_env_yaml - Conda dep had pinned version number: bioconda::damageprofiler=0.4.9
  • conda_env_yaml - Conda dep had pinned version number: bioconda::multiqc=1.13a
  • conda_env_yaml - Conda package is the latest available: bioconda::multiqc=1.13a
  • conda_env_yaml - Conda dep had pinned version number: bioconda::pmdtools=0.60
  • conda_env_yaml - Conda package is the latest available: bioconda::pmdtools=0.60
  • conda_env_yaml - Conda dep had pinned version number: bioconda::bedtools=2.30.0
  • conda_env_yaml - Conda package is the latest available: bioconda::bedtools=2.30.0
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::libiconv=1.16
  • 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::sequencetools=1.5.2
  • conda_env_yaml - Conda package is the latest available: bioconda::sequencetools=1.5.2
  • conda_env_yaml - Conda dep had pinned version number: bioconda::preseq=3.1.2
  • conda_env_yaml - Conda package is the latest available: bioconda::preseq=3.1.2
  • conda_env_yaml - Conda dep had pinned version number: bioconda::fastp=0.20.1
  • conda_env_yaml - Conda dep had pinned version number: bioconda::bamutil=1.0.15
  • conda_env_yaml - Conda package is the latest available: bioconda::bamutil=1.0.15
  • conda_env_yaml - Conda dep had pinned version number: bioconda::mtnucratio=0.7
  • conda_env_yaml - Conda package is the latest available: bioconda::mtnucratio=0.7
  • conda_env_yaml - Conda dep had pinned version number: bioconda::pysam=0.16.0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::kraken2=2.1.2
  • conda_env_yaml - Conda package is the latest available: bioconda::kraken2=2.1.2
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::pandas=1.2.4
  • conda_env_yaml - Conda dep had pinned version number: bioconda::freebayes=1.3.5
  • conda_env_yaml - Conda dep had pinned version number: bioconda::sexdeterrmine=1.1.2
  • conda_env_yaml - Conda package is the latest available: bioconda::sexdeterrmine=1.1.2
  • conda_env_yaml - Conda dep had pinned version number: bioconda::multivcfanalyzer=0.85.2
  • conda_env_yaml - Conda package is the latest available: bioconda::multivcfanalyzer=0.85.2
  • conda_env_yaml - Conda dep had pinned version number: bioconda::hops=0.35
  • conda_env_yaml - Conda package is the latest available: bioconda::hops=0.35
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::biopython=1.79
  • conda_env_yaml - Conda package is the latest available: conda-forge::biopython=1.79
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::xopen=1.1.0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::bowtie2=2.4.4
  • conda_env_yaml - Conda dep had pinned version number: bioconda::eigenstratdatabasetools=1.0.2
  • conda_env_yaml - Conda dep had pinned version number: bioconda::mapdamage2=2.2.1
  • conda_env_yaml - Conda package is the latest available: bioconda::mapdamage2=2.2.1
  • conda_env_yaml - Conda dep had pinned version number: bioconda::bbmap=38.92
  • conda_env_yaml - Conda dep had pinned version number: bioconda::bcftools=1.12
  • 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 (151 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: linting.yml
  • actions_schema_validation - Workflow validation passed: awsfulltest.yml
  • actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
  • actions_schema_validation - Workflow validation passed: branch.yml
  • actions_schema_validation - Workflow validation passed: awstest.yml
  • actions_schema_validation - Workflow validation passed: linting_comment.yml
  • actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
  • actions_schema_validation - Workflow validation passed: ci.yml
  • merge_markers - No merge markers found in pipeline files

Run details

  • nf-core/tools version 1.14
  • Run at 2022-08-25 13:18:18

jfy133
jfy133 approved these changes Aug 25, 2022
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Oops, good catch @aidaanva I'm going to make a patch branch instead and we merge into that

@jfy133 jfy133 changed the base branch from dev to patch August 25, 2022 13:16
@apeltzer apeltzer merged commit 8b7b018 into patch Sep 5, 2022
@TCLamnidis TCLamnidis deleted the tsv-documentation-fix branch May 12, 2023 07:29
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4 participants

@aidaanva @jfy133 @apeltzer