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Address release review comments #660

Merged
merged 5 commits into from
Jun 18, 2021
Merged

Address release review comments #660

merged 5 commits into from
Jun 18, 2021

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drpatelh
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github-actions bot commented Jun 18, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 936d73a

+| ✅ 114 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗  78 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: '3.2'
  • 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.transcript_fasta
  • params_used - Config variable not found in main.nf: params.additional_fasta
  • params_used - Config variable not found in main.nf: params.splicesites
  • params_used - Config variable not found in main.nf: params.gtf_extra_attributes
  • params_used - Config variable not found in main.nf: params.gtf_group_features
  • params_used - Config variable not found in main.nf: params.featurecounts_feature_type
  • params_used - Config variable not found in main.nf: params.featurecounts_group_type
  • params_used - Config variable not found in main.nf: params.gencode
  • params_used - Config variable not found in main.nf: params.save_reference
  • params_used - Config variable not found in main.nf: params.with_umi
  • params_used - Config variable not found in main.nf: params.umitools_extract_method
  • params_used - Config variable not found in main.nf: params.umitools_bc_pattern
  • params_used - Config variable not found in main.nf: params.save_umi_intermeds
  • params_used - Config variable not found in main.nf: params.clip_r1
  • params_used - Config variable not found in main.nf: params.clip_r2
  • params_used - Config variable not found in main.nf: params.three_prime_clip_r1
  • params_used - Config variable not found in main.nf: params.three_prime_clip_r2
  • params_used - Config variable not found in main.nf: params.trim_nextseq
  • params_used - Config variable not found in main.nf: params.save_trimmed
  • params_used - Config variable not found in main.nf: params.skip_trimming
  • params_used - Config variable not found in main.nf: params.remove_ribo_rna
  • params_used - Config variable not found in main.nf: params.save_non_ribo_reads
  • params_used - Config variable not found in main.nf: params.ribo_database_manifest
  • params_used - Config variable not found in main.nf: params.aligner
  • params_used - Config variable not found in main.nf: params.pseudo_aligner
  • params_used - Config variable not found in main.nf: params.seq_center
  • params_used - Config variable not found in main.nf: params.bam_csi_index
  • params_used - Config variable not found in main.nf: params.star_ignore_sjdbgtf
  • params_used - Config variable not found in main.nf: params.salmon_quant_libtype
  • params_used - Config variable not found in main.nf: params.hisat2_build_memory
  • params_used - Config variable not found in main.nf: params.stringtie_ignore_gtf
  • params_used - Config variable not found in main.nf: params.min_mapped_reads
  • params_used - Config variable not found in main.nf: params.save_merged_fastq
  • params_used - Config variable not found in main.nf: params.save_unaligned
  • params_used - Config variable not found in main.nf: params.save_align_intermeds
  • params_used - Config variable not found in main.nf: params.skip_markduplicates
  • params_used - Config variable not found in main.nf: params.skip_alignment
  • params_used - Config variable not found in main.nf: params.skip_qc
  • params_used - Config variable not found in main.nf: params.skip_bigwig
  • params_used - Config variable not found in main.nf: params.skip_stringtie
  • params_used - Config variable not found in main.nf: params.skip_fastqc
  • params_used - Config variable not found in main.nf: params.skip_preseq
  • params_used - Config variable not found in main.nf: params.skip_dupradar
  • params_used - Config variable not found in main.nf: params.skip_qualimap
  • params_used - Config variable not found in main.nf: params.skip_rseqc
  • params_used - Config variable not found in main.nf: params.skip_biotype_qc
  • params_used - Config variable not found in main.nf: params.skip_deseq2_qc
  • params_used - Config variable not found in main.nf: params.skip_multiqc
  • params_used - Config variable not found in main.nf: params.deseq2_vst
  • params_used - Config variable not found in main.nf: params.rseqc_modules
  • params_used - Config variable not found in main.nf: params.outdir
  • params_used - Config variable not found in main.nf: params.publish_dir_mode
  • params_used - Config variable not found in main.nf: params.multiqc_config
  • params_used - Config variable not found in main.nf: params.multiqc_title
  • 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.max_multiqc_email_size
  • 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.tracedir
  • params_used - Config variable not found in main.nf: params.validate_params
  • 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.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:

✅ Tests passed:

Run details

  • nf-core/tools version 1.14
  • Run at 2021-06-18 11:00:09

@drpatelh drpatelh requested a review from grst June 18, 2021 11:04
@drpatelh drpatelh merged commit 38ee463 into nf-core:dev Jun 18, 2021
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@grst grst grst approved these changes

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@drpatelh @grst