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```bash | ||
cwl-runner src/bd_rhapsody/bd_rhapsody_make_reference/make_rhap_reference_2.2.1_nodocker.cwl --help | ||
``` | ||
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||
usage: src/bd_rhapsody/bd_rhapsody_make_reference/make_rhap_reference_2.2.1_nodocker.cwl | ||
[-h] [--Archive_prefix ARCHIVE_PREFIX] | ||
[--Extra_STAR_params EXTRA_STAR_PARAMS] | ||
[--Extra_sequences EXTRA_SEQUENCES] [--Filtering_off] --Genome_fasta | ||
GENOME_FASTA --Gtf GTF [--Maximum_threads MAXIMUM_THREADS] | ||
[--Mitochondrial_Contigs MITOCHONDRIAL_CONTIGS] [--WTA_Only] | ||
[job_order] | ||
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The Reference Files Generator creates an archive containing Genome Index and | ||
Transcriptome annotation files needed for the BD Rhapsodyâ„¢ Sequencing | ||
Analysis Pipeline. The app takes as input one or more FASTA and GTF files and | ||
produces a compressed archive in the form of a tar.gz file. The archive | ||
contains:\n - STAR index\n - Filtered GTF file | ||
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||
positional arguments: | ||
job_order Job input json file | ||
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options: | ||
-h, --help show this help message and exit | ||
--Archive_prefix ARCHIVE_PREFIX | ||
A prefix for naming the compressed archive file | ||
containing the Reference genome index and annotation | ||
files. The default value is constructed based on the | ||
input Reference files. | ||
--Extra_STAR_params EXTRA_STAR_PARAMS | ||
Additional parameters to pass to STAR when building | ||
the genome index. Specify exactly like how you would | ||
on the command line. Example: --limitGenomeGenerateRAM | ||
48000 --genomeSAindexNbases 11 | ||
--Extra_sequences EXTRA_SEQUENCES | ||
Additional sequences in FASTA format to use when | ||
building the STAR index. (E.g. phiX genome) | ||
--Filtering_off By default the input Transcript Annotation files are | ||
filtered based on the gene_type/gene_biotype | ||
attribute. Only features having the following | ||
attribute values are are kept: - protein_coding - | ||
lncRNA (lincRNA and antisense for Gencode < | ||
v31/M22/Ensembl97) - IG_LV_gene - IG_V_gene - | ||
IG_V_pseudogene - IG_D_gene - IG_J_gene - | ||
IG_J_pseudogene - IG_C_gene - IG_C_pseudogene - | ||
TR_V_gene - TR_V_pseudogene - TR_D_gene - TR_J_gene - | ||
TR_J_pseudogene - TR_C_gene If you have already pre- | ||
filtered the input Annotation files and/or wish to | ||
turn-off the filtering, please set this option to | ||
True. | ||
--Genome_fasta GENOME_FASTA | ||
Reference genome file in FASTA format. The BD | ||
Rhapsodyâ„¢ Sequencing Analysis Pipeline uses GRCh38 | ||
for Human and GRCm39 for Mouse. | ||
--Gtf GTF Transcript annotation files in GTF format. The BD | ||
Rhapsodyâ„¢ Sequencing Analysis Pipeline uses Gencode | ||
v42 for Human and M31 for Mouse. | ||
--Maximum_threads MAXIMUM_THREADS | ||
The maximum number of threads to use in the pipeline. | ||
By default, all available cores are used. | ||
--Mitochondrial_Contigs MITOCHONDRIAL_CONTIGS | ||
Names of the Mitochondrial contigs in the provided | ||
Reference Genome. Fragments originating from contigs | ||
other than these are identified as 'nuclear fragments' | ||
in the ATACseq analysis pipeline. | ||
--WTA_Only Build a WTA only index, otherwise builds a WTA + ATAC | ||
index. |