Workflow: Chipseq alignment for nonhuman with qc and creating homer tag directory

Fetched 2023-01-10 01:37:52 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs chipseq_sequence chipseq_sequence: sequencing data and readgroup information alignment Alignment without BQSR chipseq_sequence->alignment unaligned per_target_intervals per_target_intervals qc WGS QC workflow nonhuman per_target_intervals->qc per_target_intervals trimming trimming trimming->alignment trimming summary_intervals summary_intervals summary_intervals->qc summary_intervals minimum_base_quality minimum_base_quality minimum_base_quality->qc minimum_base_quality reference reference reference->alignment reference reference->qc reference final_name final_name final_name->alignment final_name picard_metric_accumulation_level picard_metric_accumulation_level picard_metric_accumulation_level->qc picard_metric_accumulation_level per_base_intervals per_base_intervals per_base_intervals->qc per_base_intervals minimum_mapping_quality minimum_mapping_quality minimum_mapping_quality->qc minimum_mapping_quality insert_size_histogram insert_size_histogram summary_hs_metrics summary_hs_metrics mark_duplicates_metrics mark_duplicates_metrics per_target_hs_metrics per_target_hs_metrics flagstats flagstats per_base_coverage_metrics per_base_coverage_metrics alignment_summary_metrics alignment_summary_metrics bamcoverage_bigwig bamcoverage_bigwig gc_bias_metrics_summary gc_bias_metrics_summary per_target_coverage_metrics per_target_coverage_metrics tag_directory tag_directory insert_size_metrics insert_size_metrics gc_bias_metrics_chart gc_bias_metrics_chart wgs_metrics wgs_metrics per_base_hs_metrics per_base_hs_metrics bam bam gc_bias_metrics gc_bias_metrics bam_to_sam BAM to SAM conversion homer_tag_directory Creating the homer tag directory bam_to_sam->homer_tag_directory sam alignment->mark_duplicates_metrics alignment->bam alignment->bam_to_sam bam alignment->qc bam qc->insert_size_histogram qc->summary_hs_metrics qc->per_target_hs_metrics qc->flagstats qc->per_base_coverage_metrics qc->alignment_summary_metrics qc->bamcoverage_bigwig qc->gc_bias_metrics_summary qc->per_target_coverage_metrics qc->insert_size_metrics qc->gc_bias_metrics_chart qc->wgs_metrics qc->per_base_hs_metrics qc->gc_bias_metrics
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Inputs

ID Type Title Doc
trimming https://w3id.org/cwl/view/git/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/types/trimming_options.yml#trimming_options (Optional)
reference File
final_name String (Optional)
chipseq_sequence https://w3id.org/cwl/view/git/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/types/sequence_data.yml#sequence_data[] chipseq_sequence: sequencing data and readgroup information

chipseq_sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required.

summary_intervals https://w3id.org/cwl/view/git/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/types/labelled_file.yml#labelled_file[]
minimum_base_quality Integer (Optional)
per_target_intervals https://w3id.org/cwl/view/git/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/types/labelled_file.yml#labelled_file[]
minimum_mapping_quality Integer (Optional)
picard_metric_accumulation_level String

Steps

ID Runs Label Doc
qc WGS QC workflow nonhuman
alignment Alignment without BQSR
bam_to_sam
../tools/bam_to_sam.cwl (CommandLineTool)
BAM to SAM conversion
homer_tag_directory
../tools/homer_tag_directory.cwl (CommandLineTool)
Creating the homer tag directory

homer annotation data is too large to include in the docker image, so it requires a directory to be mounted at /opt/homerdata/ containing - config.txt - homer configuration file with directories pointing to paths like \"data/accession\" - data - folder containing homer annotation data files at WUSTL, this can be provided by providing the following in an analysis-project configuration: docker_volumes: \"/gscmnt/gc2560/core/annotation_data/homer:/opt/homerdata\" or outside the pipelines: LSF_DOCKER_VOLUMES=\"$LSF_DOCKER_VOLUMES /gscmnt/gc2560/core/annotation_data/homer:/opt/homerdata\" for compute1, instead use the path `/storage1/fs1/bga/Active/gmsroot/gc2560/core/annotation_data/homer`

Outputs

ID Type Label Doc
bam File
flagstats File
wgs_metrics File
tag_directory Directory
gc_bias_metrics File
bamcoverage_bigwig File
summary_hs_metrics File[]
insert_size_metrics File
per_base_hs_metrics File[]
gc_bias_metrics_chart File
insert_size_histogram File
per_target_hs_metrics File[]
gc_bias_metrics_summary File
mark_duplicates_metrics File
alignment_summary_metrics File
per_base_coverage_metrics File[]
per_target_coverage_metrics File[]
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Permalink: https://w3id.org/cwl/view/git/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/pipelines/chipseq_alignment_nonhuman.cwl