Workflow: pipeline-se-revstranded.cwl

Fetched 2021-04-11 15:17:12 GMT

RNA-seq pipeline - reads: PE

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Inputs

ID Type Title Doc
genome_sizes_file File

Genome sizes tab-delimited file (used in samtools)

genome_fasta_files File[]

STAR genome generate - Genome FASTA file with all the genome sequences in FASTA format

rsem_reference_files Directory

RSEM genome reference files - generated with the rsem-prepare-reference command

annotation_file File

GTF annotation file

trimmomatic_java_opts String (Optional)

JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")

STARgenomeDir Directory

STAR genome reference/indices directory.

nthreads_map Integer

Number of threads - map.

sjdb_name String
nthreads_qc Integer

Number of threads - qc.

input_fastq_read1_files File[]

Input read1 fastq files

nthreads_trimm Integer

Number of threads - trim.

trimmomatic_jar_path String

Trimmomatic Java jar file

sjdbOverhang String

Length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database.

default_adapters_file File

Adapters file

nthreads_quant Integer

Number of threads - quantification.

Steps

ID Runs Label Doc
qc
01-qc-se.cwl (Workflow)

RNA-seq 01 QC - reads: SE

trim
02-trim-se.cwl (Workflow)

RNA-seq 02 trimming - reads: SE

quant

RNA-seq 04 quantification

map
03-map-se.cwl (Workflow)

RNA-seq 03 mapping - reads: SE

Outputs

ID Type Label Doc
output_diff_counts_read1 File[]
percentage_uniq_reads_star1 File[]

Percentage of uniq reads from preseq c_curve output

bw_norm_files File[]

Normalized by RPKM bigWig files.

output_data_fastq_read1_trimmed_files File[]

Trimmed fastq files for paired read 1

output_fastqc_report_files_read1 File[]

FastQC reports in zip format for paired read 1

output_custom_adapters_read1 File[]
featurecounts_counts File[]

Normalized fragment extended reads bigWig (signal) files

read_count_mapped_star1 File[]

Read counts of the mapped BAM files after STAR pass1

read_count_mapped_star2 File[]

Read counts of the mapped BAM files after STAR pass2

read_count_transcriptome_mapped_star2 File[]

Read counts of the mapped to transcriptome BAM files after STAR pass1

star_1pass_sjdb File

SJDB from union of STAR 1st pass

generated_genome_files File (Optional)

STAR generated genome files

star1_stat_files 1598e9ef5875f9593dd3f848dad7819a[]

STAR pass-1 stat files.

transcriptome_star_stat_files 6c56185108ea46860b22dcc01eb06bab[]

STAR pass-2 aligned to transcriptome stat files.

pcr_bottleneck_coef_file File[]

PCR Bottleneck Coefficient

transcriptome_star_aligned_file File[]

STAR mapped to transcriptome sorted file.

output_trimmed_read1_fastq_read_count File[]

Trimmed read counts of paired read 1 fastq files

output_fastqc_data_files_read1 File[]

FastQC data files for paired read 1

star_aligned_sorted_file File[]

STAR mapped sorted file.

rsem_genes_files File[]

RSEM genes files

output_count_raw_reads_read1 File[]
rsem_isoforms_files File[]

RSEM isoforms files

bw_raw_files File[]

Raw bigWig files.

star2_readspergene_file File[] (Optional)

STAR pass-2 reads per gene counts file.

star2_stat_files c325011e42ced9675b42ac60b032fc27[]

STAR pass-2 stat files.

Permalink: https://w3id.org/cwl/view/git/4e568335133405d28f4b73ae11e7f51f2900dfa3/v1.0/RNA-seq_pipeline/pipeline-se-revstranded.cwl