Workflow: pipeline-pe.cwl
Fetched 2024-11-22 13:43:57 GMT
Verified with cwltool version 3.1.20221201130942
ATAC-seq pipeline - reads: PE
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| nthreads_qc | Integer |
Number of threads required for the 01-qc step |
|
| nthreads_map | Integer |
Number of threads required for the 03-map step |
|
| nthreads_quant | Integer |
Number of threads required for the 05-quantification step |
|
| nthreads_trimm | Integer |
Number of threads required for the 02-trim step |
|
| picard_jar_path | String |
Picard Java jar file |
|
| picard_java_opts | String (Optional) |
JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\") |
|
| genome_sizes_file | File |
Genome sizes tab-delimited file (used in samtools) |
|
| nthreads_peakcall | Integer |
Number of threads required for the 04-peakcall step |
|
| as_narrowPeak_file | File |
Definition narrowPeak file in AutoSql format (used in bedToBigBed) |
|
| trimmomatic_jar_path | String |
Trimmomatic Java jar file |
|
| default_adapters_file | File |
Adapters file |
|
| genome_effective_size | String |
Effective genome size used by MACS2. It can be numeric or a shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs |
|
| trimmomatic_java_opts | String (Optional) |
JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\") |
|
| input_fastq_read1_files | File[] |
Input fastq paired-end read 1 files |
|
| input_fastq_read2_files | File[] |
Input fastq paired-end read 2 files |
|
| genome_ref_first_index_file | File |
\"First index file of Bowtie reference genome with extension 1.ebwt. \ (Note: the rest of the index files MUST be in the same folder)\" |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| qc |
01-qc-pe.cwl
(Workflow)
|
ATAC-seq 01 QC - reads: PE |
|
| map |
03-map-pe.cwl
(Workflow)
|
ATAC-seq 03 mapping - reads: PE |
|
| quant |
05-quantification.cwl
(Workflow)
|
ATAC-seq - Quantification |
|
| trimm |
02-trim-pe.cwl
(Workflow)
|
ATAC-seq 02 trimming - reads: PE |
|
| peak_call |
04-peakcall-pe.cwl
(Workflow)
|
ATAC-seq 04 quantification - PE |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| map_pbc_files | File[] |
PCR Bottleneck Coefficient files (used to flag samples when pbc<0.5) |
|
| peakcall_peak_file | File[] |
Peaks in ENCODE Peak file format |
|
| map_dedup_bam_files | File[] |
Filtered BAM files (post-processing end point) |
|
| map_bowtie_log_files | File[] |
Bowtie log file with mapping stats |
|
| qc_diff_counts_read1 | File[] |
Diff file between number of raw reads and number of reads counted by FASTQC, for paired_read1 |
|
| qc_diff_counts_read2 | File[] |
Diff file between number of raw reads and number of reads counted by FASTQC, for paired_read2 |
|
| map_read_count_mapped | File[] |
Read counts of the mapped BAM files |
|
| peakcall_peak_xls_file | File[] |
Peak calling report file |
|
| quant_bigwig_raw_files | File[] |
Raw reads bigWig (signal) files |
|
| trimm_raw_counts_read1 | File[] |
Raw read counts for paired_read1 of fastq files after trimming |
|
| trimm_raw_counts_read2 | File[] |
Raw read counts for paired_read2 of fastq files after trimming |
|
| quant_bigwig_norm_files | File[] |
Normalized reads bigWig (signal) files |
|
| trimm_fastq_files_read1 | File[] |
FASTQ files for paired_read1 after trimming |
|
| trimm_fastq_files_read2 | File[] |
FASTQ files for paired_read2 after trimming |
|
| map_preseq_c_curve_files | File[] |
Preseq c_curve output files |
|
| qc_count_raw_reads_read1 | File[] |
Raw read counts of fastq files for paired_read1 after QC |
|
| qc_count_raw_reads_read2 | File[] |
Raw read counts of fastq files for paired_read2 after QC |
|
| map_mark_duplicates_files | File[] |
Summary of duplicates removed with Picard tool MarkDuplicates (for multiple reads aligned to the same positions |
|
| peakcall_peak_bigbed_file | File[] |
Peaks in bigBed format |
|
| peakcall_spp_x_cross_corr | File[] |
SPP strand cross correlation summary |
|
| peakcall_peak_summits_file | File[] |
Peaks summits in bedfile format |
|
| qc_fastqc_data_files_read1 | File[] |
FastQC data files for paired_read1 |
|
| qc_fastqc_data_files_read2 | File[] |
FastQC data files for paired_read2 |
|
| peakcall_extended_peak_file | File[] |
Extended fragment peaks in ENCODE Peak file format |
|
| qc_fastqc_report_files_read1 | File[] |
FastQC reports in zip format for paired_read1 |
|
| qc_fastqc_report_files_read2 | File[] |
FastQC reports in zip format for paired_read2 |
|
| peakcall_spp_x_cross_corr_plot | File[] |
SPP strand cross correlation plot |
|
| map_percent_mitochondrial_reads | File[] |
Percentage of mitochondrial reads |
|
| map_preseq_percentage_uniq_reads | File[] |
Preseq percentage of uniq reads |
|
| peakcall_filtered_read_count_file | File[] |
Filtered read count after peak calling |
|
| peakcall_output_unpaired_peak_file | File[] |
peakshift/phantomPeak results file using each paired mate independently |
|
| peakcall_peak_count_within_replicate | File[] |
Peak counts within replicate |
|
| peakcall_output_unpaired_peak_xls_file | File[] |
Peak calling report file (*_peaks.xls file produced by MACS2) using each paired mate independently |
|
| peakcall_output_unpaired_peak_bigbed_file | File[] |
peakshift/phantomPeak results bigbed file using each paired mate independently |
|
| peakcall_output_unpaired_peak_summits_file | File[] |
File containing peak summits using each paired mate independently |
|
| peakcall_output_unpaired_extended_peak_file | File[] |
peakshift/phantomPeak extended fragment results file using each paired mate independently |
|
| peakcall_read_in_peak_count_within_replicate | File[] |
Peak counts within replicate |
|
| peakcall_output_unpaired_filtered_read_count_file | File[] |
Filtered read count reported by MACS2 using each paired mate independently |
|
| peakcall_output_unpaired_peak_count_within_replicate | File[] |
Peak counts within replicate using each paired mate independently |
https://w3id.org/cwl/view/git/487af88ef0b971f76ecd1a215639bb47e3ee94e1/v1.0/ATAC-seq_pipeline/pipeline-pe.cwl
