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Added stand-alone executable to auto-create samplesheet from a directory of FastQ files #658

Merged
merged 4 commits into from
Jun 17, 2021
Merged

Added stand-alone executable to auto-create samplesheet from a directory of FastQ files #658

merged 4 commits into from
Jun 17, 2021

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drpatelh
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @drpatelh,

It looks like this pull-request is has been made against the drpatelh/nf-core-rnaseq 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 drpatelh/nf-core-rnaseq 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.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@drpatelh drpatelh changed the base branch from master to dev June 17, 2021 11:42
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github-actions bot commented Jun 17, 2021 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0fc2ee7

+| ✅ 114 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗  77 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.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 2021-06-17 12:46:35

JoseEspinosa
JoseEspinosa approved these changes Jun 17, 2021
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LGTM!

CHANGELOG.md
@@ -3,11 +3,12 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [Unpublished Version / DEV]
## [[3.2](https://github.com/nf-core/rnaseq/releases/tag/3.2)] - 2021-06-17
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You plan a release for tomorrow 🥁

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Oh, yes!! Not much left to do now

@drpatelh drpatelh merged commit 3a91e13 into nf-core:dev Jun 17, 2021
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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@drpatelh @JoseEspinosa