vsh/rnaseq
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
3e6bb670c56a9ccb3dcd2c9fe00b4627b873bdc1
rnaseq/target/executable/workflows/quality_control/.config.vsh.yaml
CI 3e6bb670c5 Build branch v0.1 with version v0.1.1 (0f49a3f) 
Build pipeline: vsh-ci-dev-w9454

Source commit: 0f49a3ff62

Source message: Bump version to v0.1.1
2024-10-17 17:31:01 +00:00

1646 lines
41 KiB
YAML
Raw Blame History

name: "quality_control"
namespace: "workflows"
version: "v0.1.1"
argument_groups:
- name: "Input"
arguments:
- type: "string"
name: "--id"
description: "ID of the sample"
info: null
example:
- "test"
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--strandedness"
description: "Sample strand-specificity. Must be one of unstranded, forward, reverse"
info: null
default:
- "unstranded"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--paired"
description: "Paired-end reads?"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--genome_bam"
description: "Input genome BAM file"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--genome_bam_index"
description: "Genome BAM index file"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--gene_bed"
description: "Path to BED file containing gene intervals. This will be created\
\ from the GTF file if not specified."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--gtf"
description: "GTF file"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--gtf_group_features"
description: "Define the attribute type used to group features in the GTF file\
\ when running Salmon."
info: null
default:
- "gene_id"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--gtf_extra_attributes"
description: "By default, the pipeline uses the gene_name field to obtain additional\
\ gene identifiers from the input GTF file when running Salmon."
info: null
default:
- "gene_name"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--quant_out_dir"
description: "Directory containing Salmon quantification results."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--quant_results_file"
description: "Salmon quantification file."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pseudo_quant_out_dir"
description: "Directory containing quantification results for pseudo alignment."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pseudo_salmon_quant_results_file"
description: "Quantification file from Salmon for pseudo alignment."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pseudo_kallisto_quant_results_file"
description: "Quantification file from Kallisto for pseudo alignment."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--aligner"
description: "Method used for alognment and qqunatification."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--pseudo_aligner"
description: "Method used for pseudo alignment and quantification."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--rsem_counts_gene"
description: "Expression counts on gene level"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--rsem_counts_transcripts"
description: "Expression counts on transcript level"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--skip_qc"
info: null
default:
- false
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--skip_biotype_qc"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--skip_align"
info: null
default:
- false
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--skip_pseudo_align"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--skip_preseq"
info: null
default:
- false
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--extra_preseq_args"
info: null
default:
- "-verbose -bam -seed 1"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--featurecounts_group_type"
description: "The attribute type used to group feature types in the GTF file when\
\ generating the biotype plot with featureCounts."
info: null
default:
- "gene_biotype"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--featurecounts_feature_type"
description: "By default, the pipeline assigns reads based on the 'exon' attribute\
\ within the GTF file."
info: null
default:
- "exon"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--gencode"
description: "Specify if the GTF annotation is in GENCODE format."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--biotypes_header"
info: null
default:
- "src/assets/multiqc/biotypes_header.txt"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--biotype"
description: "Biotype value to use while appending entries to GTF file when additional\
\ fasta file is provided."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--extra_featurecounts_args"
description: "Extra arguments to pass to featureCounts command in addition to\
\ defaults defined by the pipeline"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--rseqc_modules"
description: "Specify the RSeQC modules to run_wf"
info: null
default:
- "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication"
required: false
choices:
- "bam_stat"
- "inner_distance"
- "infer_experiment"
- "junction_annotation"
- "junction_saturation"
- "read_distribution"
- "read_duplication"
- "tin"
direction: "input"
multiple: true
multiple_sep: ","
- type: "integer"
name: "--sample_size"
description: "Numer of reads sampled from SAM/BAM file to infer experiment and\
\ calculate inner distance, default = 200000."
info: null
default:
- 200000
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--lower_bound_size"
description: "Lower bound of inner distance (bp). This option is used for ploting\
\ histograme, default = -250."
info: null
default:
- -250
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--upper_bound_size"
description: "Upper bound of inner distance (bp). This option is used for ploting\
\ histograme, default = 250."
info: null
default:
- 250
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--step_size"
description: "Step size (bp) of histograme of inner distance. This option is used\
\ for plotting histogram, default = 5."
info: null
default:
- 5
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--map_qual"
description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
\ reads, default = 30."
info: null
default:
- 30
required: false
min: 0
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--min_intron"
description: "Minimum intron length (bp) to call a junction, default = 50."
info: null
default:
- 50
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--min_splice_read"
description: "Minimum number of supporting reads to call a junction, default =\
\ 1."
info: null
default:
- 1
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--sampling_percentile_lower_bound"
description: "Read sampling for junction saturation starts from this percentile,\
\ must be an integer between 0 and 100, default = 5."
info: null
default:
- 5
required: false
min: 0
max: 100
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--sampling_percentile_upper_bound"
description: "Read sampling for junction saturation ends at this percentile, must\
\ be an integer between 0 and 100, default = 5."
info: null
default:
- 100
required: false
min: 0
max: 100
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--sampling_percentile_step"
description: "Read sampling for junction saturation frequency in %. Smaller value\
\ means more sampling times. Must be an integer between 0 and 100, default =\
\ 5."
info: null
default:
- 5
required: false
min: 0
max: 100
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--read_count_upper_limit"
description: "Upper limit of reads' occurence to determine read duplication. Only\
\ used for plotting, default = 500 (times)."
info: null
default:
- 500
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--minimum_coverage"
description: "Minimum number of reads mapped to a transcript to determin tin,\
\ default = 10."
info: null
default:
- 10
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--tin_sample_size"
description: "Number of equal-spaced nucleotide positions picked from mRNA. Note,\
\ if this number is larger than the length of mRNA (L), it will be halved until\
\ it's smaller than L (default = 100)"
info: null
default:
- 100
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--subtract_background"
description: "Set flag to subtract background noise (estimated from intronic reads)\
\ to determine tin. Only use this option if there are substantial intronic reads."
info: null
direction: "input"
- type: "string"
name: "--output_format"
description: "Format of the qualimap output report (PDF or HTML, default is HTML)"
info: null
default:
- "html"
required: false
choices:
- "html"
- "pdf"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--pr_bases"
description: "Number of upstream/downstream nucleotide bases to compute 5'-3'\
\ bias for qualimap (default = 100)."
info: null
default:
- 100
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--tr_bias"
description: "Number of top highly expressed transcripts to compute 5'-3' bias\
\ for qualimap (default = 1000)."
info: null
default:
- 1000
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--algorithm"
description: "Counting algorithm for qualimap (uniquely-mapped-reads (default)\
\ or proportional)."
info: null
default:
- "uniquely-mapped-reads"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--sequencing_protocol"
description: "Sequencing library protocol for qualimap (strand-specific-forward,\
\ strand-specific-reverse or non-strand-specific (default))."
info: null
default:
- "non-strand-specific"
required: false
choices:
- "non-strand-specific"
- "strand-specific-reverse"
- "strand-specific-forward"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--sorted"
description: "Setting this flag indicates that the input file is already sorted\
\ by name. If flag is not set, additional sorting by name will be performed\
\ for qualimap. Only requiredfor paired-end analysis."
info: null
direction: "input"
- type: "string"
name: "--java_memory_size"
description: "maximum Java heap memory size for qualimap, default = 4G."
info: null
default:
- "4G"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--skip_deseq2_qc"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pca_header_multiqc"
info: null
default:
- "src/assets/multiqc/deseq2_pca_header.txt"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--clustering_header_multiqc"
info: null
default:
- "src/assets/multiqc/deseq2_clustering_header.txt"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--deseq2_vst"
description: "Use vst transformation instead of rlog with DESeq2"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--extra_deseq2_args"
info: null
default:
- "--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--extra_deseq2_args2"
info: null
default:
- "star_salmon"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--multiqc_custom_config"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--multiqc_title"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--multiqc_methods_description"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--passed_trimmed_reads"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--num_trimmed_reads"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--passed_mapping"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--percent_mapped"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fastqc_zip_1"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fastqc_zip_2"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_zip_1"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_zip_2"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_log_1"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_log_2"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--sortmerna_multiqc"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--star_multiqc"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--rsem_multiqc"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--genome_bam_stats"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--genome_bam_flagstat"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--genome_bam_idxstats"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--markduplicates_multiqc"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pseudo_multiqc"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output"
arguments:
- type: "file"
name: "--preseq_output"
info: null
default:
- "$id.lc_extrap.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--bamstat_output"
description: "Path to output file (txt) of mapping quality statistics"
info: null
default:
- "$id.mapping_quality.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--strandedness_output"
description: "Path to output report (txt) of inferred strandedness"
info: null
default:
- "$id.strandedness.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--inner_dist_output_stats"
description: "output file (txt) with summary statistics of inner distances of\
\ paired reads"
info: null
default:
- "$id.inner_distance.stats"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--inner_dist_output_dist"
description: "output file (txt) with inner distances of all paired reads"
info: null
default:
- "$id.inner_distance.txt"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--inner_dist_output_freq"
description: "output file (txt) with frequencies of inner distances of all paired\
\ reads"
info: null
default:
- "$id.inner_distance_freq.txt"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--inner_dist_output_plot"
description: "output file (pdf) with histogram plot of of inner distances of all\
\ paired reads"
info: null
default:
- "$id.inner_distance_plot.pdf"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--inner_dist_output_plot_r"
description: "output file (R) with script of histogram plot of of inner distances\
\ of all paired reads"
info: null
default:
- "$id.inner_distance_plot.r"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--junction_annotation_output_log"
description: "output log of junction annotation script"
info: null
default:
- "$id.junction_annotation.log"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--junction_annotation_output_plot_r"
description: "R script to generate splice_junction and splice_events plot"
info: null
default:
- "$id.junction_annotation_plot.r"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--junction_annotation_output_junction_bed"
description: "junction annotation file (bed format)"
info: null
default:
- "$id.junction_annotation.bed"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--junction_annotation_output_junction_interact"
description: "interact file (bed format) of junctions. Can be uploaded to UCSC\
\ genome browser or converted to bigInteract (using bedToBigBed program) for\
\ visualization."
info: null
default:
- "$id.junction_annotation.Interact.bed"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--junction_annotation_output_junction_sheet"
description: "junction annotation file (xls format)"
info: null
default:
- "$id.junction_annotation.xls"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--junction_annotation_output_splice_events_plot"
description: "plot of splice events (pdf)"
info: null
default:
- "$id.splice_events.pdf"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--junction_annotation_output_splice_junctions_plot"
description: "plot of junctions (pdf)"
info: null
default:
- "$id.splice_junctions_plot.pdf"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--junction_saturation_output_plot_r"
description: "r script to generate junction_saturation_plot plot"
info: null
default:
- "$id.junction_saturation_plot.r"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--junction_saturation_output_plot"
description: "plot of junction saturation (pdf"
info: null
default:
- "$id.junction_saturation_plot.pdf"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--read_distribution_output"
description: "output file (txt) of read distribution analysis."
info: null
default:
- "$id.read_distribution.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--read_duplication_output_duplication_rate_plot_r"
description: "R script for generating duplication rate plot"
info: null
default:
- "$id.duplication_rate_plot.r"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--read_duplication_output_duplication_rate_plot"
description: "duplication rate plot (pdf)"
info: null
default:
- "$id.duplication_rate_plot.pdf"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--read_duplication_output_duplication_rate_mapping"
description: "Summary of mapping-based read duplication"
info: null
default:
- "$id.duplication_rate_mapping.xls"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--read_duplication_output_duplication_rate_sequence"
description: "Summary of sequencing-based read duplication"
info: null
default:
- "$id.duplication_rate_sequencing.xls"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--tin_output_summary"
description: "summary statistics (txt) of calculated TIN metrics"
info: null
default:
- "$id.tin_summary.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--tin_output_metrics"
description: "file with TIN metrics (xls)"
info: null
default:
- "$id.tin.xls"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--dupradar_output_dupmatrix"
description: "path to output file (txt) of duplicate tag counts"
info: null
default:
- "$id.dup_matrix.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--dupradar_output_dup_intercept_mqc"
description: "path to output file (txt) of multiqc intercept value DupRadar"
info: null
default:
- "$id.dup_intercept_mqc.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--dupradar_output_duprate_exp_boxplot"
description: "path to output file (pdf) of distribution of expression box plot"
info: null
default:
- "$id.duprate_exp_boxplot.pdf"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--dupradar_output_duprate_exp_densplot"
description: "path to output file (pdf) of 2D density scatter plot of duplicate\
\ tag counts"
info: null
default:
- "$id.duprate_exp_densityplot.pdf"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--dupradar_output_duprate_exp_denscurve_mqc"
description: "path to output file (pdf) of density curve of gene duplication multiqc"
info: null
default:
- "$id.duprate_exp_density_curve_mqc.pdf"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--dupradar_output_expression_histogram"
description: "path to output file (pdf) of distribution of RPK values per gene\
\ histogram"
info: null
default:
- "$id.expression_hist.pdf"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--dupradar_output_intercept_slope"
info: null
default:
- "$id.intercept_slope.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--qualimap_output_pdf"
info: null
default:
- "$id.qualimap_output.pdf"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--qualimap_output_dir"
info: null
default:
- "$id.qualimap_output"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--deseq2_output"
info: null
default:
- "deseq2"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--deseq2_output_pseudo"
info: null
default:
- "deseq2_pseudo"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--multiqc_report"
info: null
default:
- "multiqc_report.html"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--multiqc_data"
info: null
default:
- "multiqc_data"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--multiqc_plots"
info: null
default:
- "multiqc_plots"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--featurecounts"
info: null
default:
- "$id.featureCounts.txt"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--featurecounts_summary"
info: null
default:
- "$id.featureCounts.txt.summary"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--featurecounts_multiqc"
info: null
default:
- "$id.featureCounts_mqc.tsv"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--featurecounts_rrna_multiqc"
info: null
default:
- "$id.featureCounts_rrna_mqc.tsv"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--tpm_gene"
info: null
default:
- "salmon.merged.gene_tpm.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--counts_gene"
info: null
default:
- "salmon.merged.gene_counts.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--counts_gene_length_scaled"
info: null
default:
- "salmon.merged.gene_counts_length_scaled.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--counts_gene_scaled"
info: null
default:
- "salmon.merged.gene_counts_scaled.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--tpm_transcript"
info: null
default:
- "salmon.merged.transcript_tpm.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--counts_transcript"
info: null
default:
- "salmon.merged.transcript_counts.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--quant_merged_summarizedexperiment"
info: null
default:
- "salmon_merged_summarizedexperiment"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pseudo_tpm_gene"
info: null
default:
- "pseudo_gene_tpm.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pseudo_counts_gene"
info: null
default:
- "pseudo_gene_counts.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pseudo_counts_gene_length_scaled"
info: null
default:
- "pseudo_gene_counts_length_scaled.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pseudo_counts_gene_scaled"
info: null
default:
- "pseudo_gene_counts_scaled.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pseudo_tpm_transcript"
info: null
default:
- "pseudo_transcript_tpm.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pseudo_counts_transcript"
info: null
default:
- "pseudo_transcript_counts.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pseudo_quant_merged_summarizedexperiment"
info: null
default:
- "pseudo_quant_merged_summarizedexperiment"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "nextflow_script"
path: "main.nf"
is_executable: true
entrypoint: "run_wf"
description: "A subworkflow for the final quality control stage of the nf-core/rnaseq\
\ pipeline.\n"
info: null
status: "enabled"
requirements:
commands:
- "ps"
dependencies:
- name: "rseqc/rseqc_bamstat"
repository:
type: "local"
- name: "rseqc/rseqc_inferexperiment"
repository:
type: "local"
- name: "rseqc/rseqc_innerdistance"
repository:
type: "local"
- name: "rseqc/rseqc_junctionannotation"
repository:
type: "local"
- name: "rseqc/rseqc_junctionsaturation"
repository:
type: "local"
- name: "rseqc/rseqc_readdistribution"
repository:
type: "local"
- name: "rseqc/rseqc_readduplication"
repository:
type: "local"
- name: "rseqc/rseqc_tin"
repository:
type: "local"
- name: "dupradar"
repository:
type: "local"
- name: "qualimap"
repository:
type: "local"
- name: "preseq_lcextrap"
repository:
type: "local"
- name: "featurecounts"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "multiqc_custom_biotype"
repository:
type: "local"
- name: "deseq2_qc"
repository:
type: "local"
- name: "prepare_multiqc_input"
repository:
type: "local"
- name: "multiqc"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "rsem/rsem_merge_counts"
repository:
type: "local"
- name: "workflows/merge_quant_results"
repository:
type: "local"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "native"
id: "native"
build_info:
config: "src/workflows/quality_control/config.vsh.yaml"
runner: "executable"
engine: "native"
output: "target/executable/workflows/quality_control"
executable: "target/executable/workflows/quality_control/quality_control"
viash_version: "0.9.0"
git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/rseqc/rseqc_bamstat"
- "target/nextflow/rseqc/rseqc_inferexperiment"
- "target/nextflow/rseqc/rseqc_innerdistance"
- "target/nextflow/rseqc/rseqc_junctionannotation"
- "target/nextflow/rseqc/rseqc_junctionsaturation"
- "target/nextflow/rseqc/rseqc_readdistribution"
- "target/nextflow/rseqc/rseqc_readduplication"
- "target/nextflow/rseqc/rseqc_tin"
- "target/nextflow/dupradar"
- "target/nextflow/qualimap"
- "target/nextflow/preseq_lcextrap"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts"
- "target/nextflow/multiqc_custom_biotype"
- "target/nextflow/deseq2_qc"
- "target/nextflow/prepare_multiqc_input"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc"
- "target/nextflow/rsem/rsem_merge_counts"
- "target/nextflow/workflows/merge_quant_results"
package_config:
name: "rnaseq"
version: "v0.1.1"
info:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
dest: "testData"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
\ := '$id'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh"
Reference in New Issue View Git Blame Copy Permalink