- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
---|---|---|---|
reads | File[] | ||
assembler | String | ||
sequences | File | ||
output_dest | String | ||
min_contig_length | Integer |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
readfq |
readfq.cwl
(CommandLineTool)
|
usage: kseq_fastq_base input.fastq.gz [input2.fastq.gz input3.fastq.gz ...] |
|
bwa_mem |
bwa-mem.cwl
(CommandLineTool)
|
Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq] |
|
bwa_index |
bwa-index.cwl
(CommandLineTool)
|
Usage: bwa index [options] <in.fasta> |
|
metabat_jgi |
metabat-jgi-summarise.cwl
(CommandLineTool)
|
Usage: jgi_summarize_bam_contig_depths <options> sortedBam1 [ sortedBam2 ...]
where options include:
--outputDepth arg The file to put the contig by bam depth matrix (default: STDOUT)
--percentIdentity arg The minimum end-to-end % identity of qualifying reads (default: 97)
--pairedContigs arg The file to output the sparse matrix of contigs which paired reads span (default: none)
--unmappedFastq arg The prefix to output unmapped reads from each bam file suffixed by 'bamfile.bam.fastq.gz'
--noIntraDepthVariance Do not include variance from mean depth along the contig
--showDepth Output a .depth file per bam for each contig base
--minMapQual arg The minimum mapping quality necessary to count the read as mapped (default: 0)
--weightMapQual arg Weight per-base depth based on the MQ of the read (i.e uniqueness) (default: 0.0 (disabled))
--includeEdgeBases When calculating depth & variance, include the 1-readlength edges (off by default)
--maxEdgeBases When calculating depth & variance, and not --includeEdgeBases, the maximum length (default:75)
--referenceFasta arg The reference file. (It must be the same fasta that bams used) |
|
stats_report |
stats-report.cwl
(CommandLineTool)
|
usage: gen_coverage_report.py [-h] output coverage_file base_count |
|
samtools_sort |
samtools-sort.cwl
(CommandLineTool)
|
samtools-sort.cwl is developed for CWL consortium
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-o FILE Write final output to FILE rather than standard output
-O FORMAT Write output as FORMAT ('sam'/'bam'/'cram') (either -O or
-T PREFIX Write temporary files to PREFIX.nnnn.bam -T is required)
-@ INT Set number of sorting and compression threads [1] |
|
samtools_view |
samtools-view.cwl
(CommandLineTool)
|
samtools-view.cwl is developed for CWL consortium
Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...] |
|
samtools_index |
samtools-index.cwl
(CommandLineTool)
|
samtools-index.cwl is developed for CWL consortium |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
logfile | File | ||
bwa_mem_output | File | ||
bwa_index_output | File | ||
samtools_sort_output | File | ||
samtools_view_output | File | ||
samtools_index_output | File | ||
metabat_coverage_output | File |
https://w3id.org/cwl/view/git/77abc2651e7ccd8f1e05f5bbdb009b13a935c2b9/cwl/stats/stats.cwl