Preprocessing_Tasks
DemuxMasSeqDataByIndex
- description
- This workflow will split MAS-seq data that is indexed with a 10bp sequence at the 3' end.
- author
- Jonn Smith
- jonn@broadinstitute.org
Inputs
Required
array_bam(File, required): Bam file containing annotated MAS-seq array reads that contain a 10bp index near the 3' end..
Outputs
demux_i1(File)demux_i2(File)demux_i3(File)demux_i4(File)demux_ambiguous(File)log_file(File)
ConvertSplicedBamToGff
- description
- Convert a given splice aligned bam file into a gff file.
- author
- Jonn Smith
- jonn@broadinstitute.org
Inputs
Required
bam(File, required): Bamfile to be converted to gff.
Optional
runtime_attr_override(RuntimeAttr?)
Outputs
gff(File)
GffCompare
- description
- Compare two GFF files
- author
- Jonn Smith
- jonn@broadinstitute.org
Inputs
Required
gff_query(File, required): Gff file to be used as a query (compared against the gff_ref).gff_ref(File, required): Gff file to be used as a reference.ref_fasta(File, required): Reference fasta file.
Optional
ref_fasta_index(File?): Reference fasta file index.runtime_attr_override(RuntimeAttr?)
Defaults
prefix(String, default="out")
Outputs
refmap(File)tmap(File)tracking(File)loci(File)annotated_gtf(File)stats(File)log(File)
RestoreOriginalReadNames
- description
- Copies the contents of the XM tag to the read name and sets the XM tag to the read name.
- author
- Jonn Smith
- jonn@broadinstitute.org
Inputs
Required
bam(File, required): Bam file in which to restore the original read names.
Optional
runtime_attr_override(RuntimeAttr?)
Defaults
prefix(String, default="out")
Outputs
bam_out(File)bai_out(File)
CorrectUmisWithSetCover
- description
- Corrects the UMIs in the given reads using a set cover algorithm
- author
- Jonn Smith
- jonn@broadinstitute.org
Inputs
Required
bam(File, required): Bam file for which to correct UMIs.
Optional
runtime_attr_override(RuntimeAttr?)
Defaults
is_extracted(Boolean, default=true)prefix(String, default="out"): Prefix to assign to output files.
Outputs
corrected_umi_reads(File)corrected_umi_reads_index(File)uncorrected_umi_reads(File)