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emmarousseau / biobox Public

forked from viash-hub/biobox

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Test components

Merge branch 'viash-hub:main' into main #195

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Merge branch 'viash-hub:main' into main

Merge branch 'viash-hub:main' into main #195

Summary
Jobs
- List components to test
  
  Test (rsem_calculate_expression, rsem, src/rsem/rsem_calculate_expression/config.vsh.yaml, src/rs...
  
  Test (rsem_prepare_reference, rsem, src/rsem/rsem_prepare_reference/config.vsh.yaml, src/rsem/rse...
  
  Test (trimgalore, src/trimgalore/config.vsh.yaml, src/trimgalore/, bash_script, trimgalore)
  
  Test (snpeff, src/snpeff/config.vsh.yaml, src/snpeff/, bash_script, snpeff)
  
  Test (nanoplot, src/nanoplot/config.vsh.yaml, src/nanoplot/, bash_script, nanoplot)
  
  Test (salmon_quant, salmon, src/salmon/salmon_quant/config.vsh.yaml, src/salmon/salmon_quant/, ba...
  
  Test (salmon_index, salmon, src/salmon/salmon_index/config.vsh.yaml, src/salmon/salmon_index/, ba...
  
  Test (seqtk_subseq, seqtk, src/seqtk/seqtk_subseq/config.vsh.yaml, src/seqtk/seqtk_subseq/, bash_...
  
  Test (seqtk_sample, seqtk, src/seqtk/seqtk_sample/config.vsh.yaml, src/seqtk/seqtk_sample/, bash_...
  
  Test (qualimap_rnaseq, qualimap, src/qualimap/qualimap_rnaseq/config.vsh.yaml, src/qualimap/quali...
  
  Test (rseqc_inferexperiment, rseqc, src/rseqc/rseqc_inferexperiment/config.vsh.yaml, src/rseqc/rs...
  
  Test (rseqc_inner_distance, rseqc, src/rseqc/rseqc_inner_distance/config.vsh.yaml, src/rseqc/rseq...
  
  Test (rseqc_bamstat, rseqc, src/rseqc/rseqc_bamstat/config.vsh.yaml, src/rseqc/rseqc_bamstat/, ba...
  
  Test (cutadapt, src/cutadapt/config.vsh.yaml, src/cutadapt/, bash_script, cutadapt)
  
  Test (bedtools_links, bedtools, src/bedtools/bedtools_links/config.vsh.yaml, src/bedtools/bedtool...
  
  Test (bedtools_bed12tobed6, bedtools, src/bedtools/bedtools_bed12tobed6/config.vsh.yaml, src/bedt...
  
  Test (bedtools_genomecov, bedtools, src/bedtools/bedtools_genomecov/config.vsh.yaml, src/bedtools...
  
  Test (bedtools_sort, bedtools, src/bedtools/bedtools_sort/config.vsh.yaml, src/bedtools/bedtools_...
  
  Test (bedtools_groupby, bedtools, src/bedtools/bedtools_groupby/config.vsh.yaml, src/bedtools/bed...
  
  Test (bedtools_merge, bedtools, src/bedtools/bedtools_merge/config.vsh.yaml, src/bedtools/bedtool...
  
  Test (bedtools_bamtofastq, bedtools, src/bedtools/bedtools_bamtofastq/config.vsh.yaml, src/bedtoo...
  
  Test (bedtools_getfasta, bedtools, src/bedtools/bedtools_getfasta/config.vsh.yaml, src/bedtools/b...
  
  Test (bedtools_bedtobam, bedtools, src/bedtools/bedtools_bedtobam/config.vsh.yaml, src/bedtools/b...
  
  Test (bedtools_intersect, bedtools, src/bedtools/bedtools_intersect/config.vsh.yaml, src/bedtools...
  
  Test (bedtools_bamtobed, bedtools, src/bedtools/bedtools_bamtobed/config.vsh.yaml, src/bedtools/b...
  
  Test (featurecounts, src/featurecounts/config.vsh.yaml, src/featurecounts/, bash_script, featurec...
  
  Test (fastqc, src/fastqc/config.vsh.yaml, src/fastqc/, bash_script, fastqc)
  
  Test (multiqc, src/multiqc/config.vsh.yaml, src/multiqc/, bash_script, multiqc)
  
  Test (fq_subsample, src/fq_subsample/config.vsh.yaml, src/fq_subsample/, bash_script, fq_subsample)
  
  Test (falco, src/falco/config.vsh.yaml, src/falco/, bash_script, falco)
  
  Test (bd_rhapsody_sequence_analysis, bd_rhapsody, src/bd_rhapsody/bd_rhapsody_sequence_analysis/c...
  
  Test (bd_rhapsody_make_reference, bd_rhapsody, src/bd_rhapsody/bd_rhapsody_make_reference/config....
  
  Test (agat_convert_sp_gxf2gxf, agat, src/agat/agat_convert_sp_gxf2gxf/config.vsh.yaml, src/agat/a...
  
  Test (agat_sp_merge_annotations, agat, src/agat/agat_sp_merge_annotations/config.vsh.yaml, src/ag...
  
  Test (agat_convert_sp_gff2tsv, agat, src/agat/agat_convert_sp_gff2tsv/config.vsh.yaml, src/agat/a...
  
  Test (agat_convert_genscan2gff, agat, src/agat/agat_convert_genscan2gff/config.vsh.yaml, src/agat...
  
  Test (agat_sp_filter_feature_from_kill_list, agat, src/agat/agat_sp_filter_feature_from_kill_list...
  
  Test (agat_sp_add_introns, agat, src/agat/agat_sp_add_introns/config.vsh.yaml, src/agat/agat_sp_a...
  
  Test (agat_convert_bed2gff, agat, src/agat/agat_convert_bed2gff/config.vsh.yaml, src/agat/agat_co...
  
  Test (agat_sp_statistics, agat, src/agat/agat_sp_statistics/config.vsh.yaml, src/agat/agat_sp_sta...
  
  Test (agat_convert_mfannot2gff, agat, src/agat/agat_convert_mfannot2gff/config.vsh.yaml, src/agat...
  
  Test (agat_convert_embl2gff, agat, src/agat/agat_convert_embl2gff/config.vsh.yaml, src/agat/agat_...
  
  Test (agat_sq_stat_basic, agat, src/agat/agat_sq_stat_basic/config.vsh.yaml, src/agat/agat_sq_sta...
  
  Test (agat_convert_sp_gff2gtf, agat, src/agat/agat_convert_sp_gff2gtf/config.vsh.yaml, src/agat/a...
  
  Test (umi_tools_prepareforrsem, umi_tools, src/umi_tools/umi_tools_prepareforrsem/config.vsh.yaml...
  
  Test (umi_tools_extract, umi_tools, src/umi_tools/umi_tools_extract/config.vsh.yaml, src/umi_tool...
  
  Test (umi_tools_dedup, umi_tools, src/umi_tools/umi_tools_dedup/config.vsh.yaml, src/umi_tools/um...
  
  Test (arriba, src/arriba/config.vsh.yaml, src/arriba/, bash_script, arriba)
  
  Test (gffread, src/gffread/config.vsh.yaml, src/gffread/, bash_script, gffread)
  
  Test (lofreq_indelqual, lofreq, src/lofreq/indelqual/config.vsh.yaml, src/lofreq/indelqual/, bash...
  
  Test (lofreq_call, lofreq, src/lofreq/call/config.vsh.yaml, src/lofreq/call/, bash_script, lofreq...
  
  Test (bcl_convert, src/bcl_convert/config.vsh.yaml, src/bcl_convert/, bash_script, bcl_convert)
  
  Test (samtools_faidx, samtools, src/samtools/samtools_faidx/config.vsh.yaml, src/samtools/samtool...
  
  Test (samtools_collate, samtools, src/samtools/samtools_collate/config.vsh.yaml, src/samtools/sam...
  
  Test (samtools_sort, samtools, src/samtools/samtools_sort/config.vsh.yaml, src/samtools/samtools_...
  
  Test (samtools_flagstat, samtools, src/samtools/samtools_flagstat/config.vsh.yaml, src/samtools/s...
  
  Test (samtools_fastq, samtools, src/samtools/samtools_fastq/config.vsh.yaml, src/samtools/samtool...
  
  Test (samtools_view, samtools, src/samtools/samtools_view/config.vsh.yaml, src/samtools/samtools_...
  
  Test (samtools_idxstats, samtools, src/samtools/samtools_idxstats/config.vsh.yaml, src/samtools/s...
  
  Test (samtools_fasta, samtools, src/samtools/samtools_fasta/config.vsh.yaml, src/samtools/samtool...
  
  Test (samtools_stats, samtools, src/samtools/samtools_stats/config.vsh.yaml, src/samtools/samtool...
  
  Test (samtools_index, samtools, src/samtools/samtools_index/config.vsh.yaml, src/samtools/samtool...
  
  Test (pear, src/pear/config.vsh.yaml, src/pear/, bash_script, pear)
  
  Test (kallisto_index, kallisto, src/kallisto/kallisto_index/config.vsh.yaml, src/kallisto/kallist...
  
  Test (kallisto_quant, kallisto, src/kallisto/kallisto_quant/config.vsh.yaml, src/kallisto/kallist...
  
  Test (star_genome_generate, star, src/star/star_genome_generate/config.vsh.yaml, src/star/star_ge...
  
  Test (star_align_reads, star, src/star/star_align_reads/config.vsh.yaml, src/star/star_align_read...
  
  Test (busco_list_datasets, busco, src/busco/busco_list_datasets/config.vsh.yaml, src/busco/busco_...
  
  Test (busco_download_datasets, busco, src/busco/busco_download_datasets/config.vsh.yaml, src/busc...
  
  Test (busco_run, busco, src/busco/busco_run/config.vsh.yaml, src/busco/busco_run/, bash_script, b...
  
  Test (fastp, src/fastp/config.vsh.yaml, src/fastp/, bash_script, fastp)
  
  Test (bbmap_bbsplit, bbmap, src/bbmap_bbsplit/config.vsh.yaml, src/bbmap_bbsplit/, bash_script, b...
  
  Test (bcftools_norm, bcftools, src/bcftools/bcftools_norm/config.vsh.yaml, src/bcftools/bcftools_...
  
  Test (bcftools_annotate, bcftools, src/bcftools/bcftools_annotate/config.vsh.yaml, src/bcftools/b...
  
  Test (bcftools_concat, bcftools, src/bcftools/bcftools_concat/config.vsh.yaml, src/bcftools/bcfto...
  
  Test (bcftools_stats, bcftools, src/bcftools/bcftools_stats/config.vsh.yaml, src/bcftools/bcftool...
  
  Test (bcftools_sort, bcftools, src/bcftools/bcftools_sort/config.vsh.yaml, src/bcftools/bcftools_...
  
  Test (sortmerna, src/sortmerna/config.vsh.yaml, src/sortmerna/, bash_script, sortmerna)
Run details
- Usage
- Workflow file

Usage Workflow file

test / Test (samtools_fasta, samtools, src/samtools/samtools_fasta/config.vsh.yaml, src/samtools/samtool...

succeeded Nov 7, 2024 in 3m 20s

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