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Fix Python script to auto-create samplesheet #211

Merged
merged 6 commits into from
Jun 18, 2021
Merged

Fix Python script to auto-create samplesheet #211

merged 6 commits into from
Jun 18, 2021

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drpatelh
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@drpatelh drpatelh commented Jun 18, 2021 •
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@drpatelh drpatelh requested a review from JoseEspinosa June 18, 2021 12:16
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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 59b2dc1

+| ✅ 116 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗  81 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
  • 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:

✅ Tests passed:

Run details

  • nf-core/tools version 1.14
  • Run at 2021-06-18 12:29:17

JoseEspinosa
JoseEspinosa approved these changes Jun 18, 2021
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LGTM! 🎸

bin/fastq_dir_to_samplesheet.py
sanitise_name = args.SANITISE_NAME,
sanitise_name_delimiter = args.SANITISE_NAME_DELIMITER,
sanitise_name_index = args.SANITISE_NAME_INDEX
fastq_dir=args.FASTQ_DIR,
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Don't want to contradict black but I find readable the previous version 😝

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😏 Me too!

@JoseEspinosa JoseEspinosa merged commit c52ba10 into nf-core:dev Jun 18, 2021
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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2 participants
@drpatelh @JoseEspinosa