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Add and fix ECLint in pipeline #629

Merged
merged 18 commits into from
May 12, 2021
Merged

Add and fix ECLint in pipeline #629

merged 18 commits into from
May 12, 2021

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drpatelh
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Will fix here as a replacement for #627 because it will be easier to systematically add changes to see where that Groovy compilation error in that PR is coming from. Will fix other stuff like comments at the same time like I have done in nf-core/viralrecon#188

@drpatelh drpatelh mentioned this pull request May 11, 2021
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@drpatelh drpatelh requested a review from ewels May 11, 2021 23:57
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github-actions bot commented May 11, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 92e96a7

+| ✅ 115 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: '3.1'
  • params_used - Config variable not found in main.nf: params.input
  • params_used - Config variable not found in main.nf: params.skip_sra_fastq_download
  • 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.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 2021-05-12 00:02:04

@drpatelh
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Done 🛏️ 🤞🏽

@JoseEspinosa JoseEspinosa requested review from JoseEspinosa and removed request for JoseEspinosa May 12, 2021 09:24
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JoseEspinosa approved these changes May 12, 2021
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@JoseEspinosa JoseEspinosa left a comment

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Looks beautiful! 😍

conf/modules.config
* suffix = File name suffix for output files.
*
*/
========================================================================================
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So clean 😍

@drpatelh drpatelh merged commit f040ba5 into nf-core:dev May 12, 2021
This was referenced May 12, 2021
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

@ewels ewels Awaiting requested review from ewels

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@drpatelh @JoseEspinosa