From 2f95be6304b126adf1922cd40ce6e04da7706702 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 23 Aug 2021 18:29:25 -0400 Subject: [PATCH 1/8] Adding downsamplesam --- docs/gatk/gatk_downsamplesam_4.1.8.1.md | 113 ++++++++ gatk_downsamplesam_4.1.8.1/example_inputs.yml | 29 ++ .../gatk_downsamplesam_4.1.8.1.cwl | 270 ++++++++++++++++++ 3 files changed, 412 insertions(+) create mode 100644 docs/gatk/gatk_downsamplesam_4.1.8.1.md create mode 100644 gatk_downsamplesam_4.1.8.1/example_inputs.yml create mode 100644 gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl diff --git a/docs/gatk/gatk_downsamplesam_4.1.8.1.md b/docs/gatk/gatk_downsamplesam_4.1.8.1.md new file mode 100644 index 00000000..b0f093d9 --- /dev/null +++ b/docs/gatk/gatk_downsamplesam_4.1.8.1.md @@ -0,0 +1,113 @@ +# ApplyBQSR v4.1.8.1 + +## Version of tools in [docker image ](https://hub.docker.com/r/broadinstitute/gatk) + +| Tool | Version | Location | +| :--- | :--- | :--- | +| GATK | 4.1.8.1 | [https://github.com/broadinstitute/gatk/releases/tag/4.1.8.1](https://github.com/broadinstitute/gatk/releases/tag/4.1.8.1) | + +[![](https://img.shields.io/badge/version-4.1.8.1-blue)](https://github.com/broadinstitute/gatk/releases/tag/4.1.8.1) + +## CWL + +* CWL specification 1.0 +* Use example\_inputs.yml to see the inputs to the cwl +* Example Command using [toil](https://toil.readthedocs.io): + +```bash + > toil-cwl-runner gatk_downsamplesam_4.1.8.1.cwl example_inputs.yml +``` + +**If at MSK, using the JUNO cluster you can use the following command** + +```bash +#Using CWLTOOL +> cwltool --singularity --non-strict gatk_downsamplesam_4.1.8.1.cwl inputs.yaml + +#Using toil-cwl-runner +> mkdir run_directory +> toil-cwl-runner --singularity --logFile path/to/run_directory/cwltoil.log --jobStore path/to/jobStore --batchSystem lsf --workDir /path/to/run_directory --outdir /path/to/run_directory --writeLogs /path/to/run_directory --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 gatk_downsamplesam_4.1.8.1.cwl inputs.yaml > file.stdout 2> file.stderr & +``` + +## Usage + +\`\`\`bash + +> toil-cwl-runner gatk_downsamplesam_4.1.8.1.cwl --help + +usage: gatk_downsamplesam_4.1.8.1.cwl [-h] --input INPUT --reference REFERENCE + [--output_file_name OUTPUT_FILE_NAME] + [--output_file_name_metrics OUTPUT_FILE_NAME_METRICS] + [--probability PROBABILITY] + [--random_seed RANDOM_SEED] + [--strategy STRATEGY] + [--arguments_file ARGUMENTS_FILE] + [--cloud-index-prefetch-buffer CLOUD_INDEX_PREFETCH_BUFFER] + [--cloud_prefetch_buffer CLOUD_PREFETCH_BUFFER] + [--create_output_bam_index] + [--create_output_bam_md5] + [--disable_bam_index_caching] + [--disable_read_filter DISABLE_READ_FILTER] + [--disable_sequence_dictionary_validation] + [--exclude_intervals EXCLUDE_INTERVALS] + [--gatk_config_file GATK_CONFIG_FILE] + [--gcs_max_retries GCS_MAX_RETRIES] + [--gcs_project_for_requester_pays GCS_PROJECT_FOR_REQUESTER_PAYS] + [--QUIET] [--read_filter READ_FILTER] + [--read_index READ_INDEX] + [--seconds_between_progress_updates SECONDS_BETWEEN_PROGRESS_UPDATES] + [--lenient] + [--number_of_threads NUMBER_OF_THREADS] + [--memory_per_job MEMORY_PER_JOB] + [--memory_overhead MEMORY_OVERHEAD] + [--temporary_directory TEMPORARY_DIRECTORY] + [job_order] + +positional arguments: + job_order Job input json file + +optional arguments: + -h, --help show this help message and exit + --input INPUT BAM/SAM file containing reads + --reference REFERENCE + Reference sequence file + --output_file_name OUTPUT_FILE_NAME + Output file name. Not Required + --output_file_name_metrics OUTPUT_FILE_NAME_METRICS + Output file name for metrics file. Not Required + --probability PROBABILITY + The probability of keeping any individual read, + between 0 and 1. + --random_seed RANDOM_SEED + Random seed used for deterministic results. Setting to + null will cause multiple invocations to produce + different results. + --strategy STRATEGY The --STRATEGY argument is an enumerated type + (Strategy), which can have one of the following + values: HighAccuracy ConstantMemory Chained default + Strategy ConstantMemory + --arguments_file ARGUMENTS_FILE + --cloud-index-prefetch-buffer CLOUD_INDEX_PREFETCH_BUFFER + --cloud_prefetch_buffer CLOUD_PREFETCH_BUFFER + --create_output_bam_index + --create_output_bam_md5 + --disable_bam_index_caching + --disable_read_filter DISABLE_READ_FILTER + Read filters to be disabled before analysis + --disable_sequence_dictionary_validation + --exclude_intervals EXCLUDE_INTERVALS + --gatk_config_file GATK_CONFIG_FILE + --gcs_max_retries GCS_MAX_RETRIES + --gcs_project_for_requester_pays GCS_PROJECT_FOR_REQUESTER_PAYS + --QUIET + --read_filter READ_FILTER + --read_index READ_INDEX + --seconds_between_progress_updates SECONDS_BETWEEN_PROGRESS_UPDATES + --lenient + --number_of_threads NUMBER_OF_THREADS + --memory_per_job MEMORY_PER_JOB + --memory_overhead MEMORY_OVERHEAD + --temporary_directory TEMPORARY_DIRECTORY + Default value: null. + + diff --git a/gatk_downsamplesam_4.1.8.1/example_inputs.yml b/gatk_downsamplesam_4.1.8.1/example_inputs.yml new file mode 100644 index 00000000..dda5b747 --- /dev/null +++ b/gatk_downsamplesam_4.1.8.1/example_inputs.yml @@ -0,0 +1,29 @@ +QUIET: null +arguments_file: null +cloud-index-prefetch-buffer: null +cloud_prefetch_buffer: null +create_output_bam_index: null +create_output_bam_md5: null +disable_bam_index_caching: null +disable_read_filter: null +disable_sequence_dictionary_validation: null +exclude_intervals: null +gatk_config_file: null +gcs_max_retries: null +gcs_project_for_requester_pays: null +input: null +lenient: null +memory_overhead: null +memory_per_job: null +number_of_threads: null +output_file_name: null +output_file_name_metrics: null +probability: null +random_seed: null +read_filter: null +read_index: null +reference: null +seconds_between_progress_updates: null +strategy: null +temporary_directory: null + diff --git a/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl b/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl new file mode 100644 index 00000000..d235bc0e --- /dev/null +++ b/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl @@ -0,0 +1,270 @@ +class: CommandLineTool +cwlVersion: v1.0 +$namespaces: + dct: 'http://purl.org/dc/terms/' + doap: 'http://usefulinc.com/ns/doap#' + foaf: 'http://xmlns.com/foaf/0.1/' + sbg: 'https://www.sevenbridges.com/' +id: gatk_downsamplesam_4_1_8_1 +baseCommand: + - gatk + - DownsampleSam +inputs: + - id: input + type: File + inputBinding: + position: 3 + prefix: '--input' + doc: BAM/SAM file containing reads + secondaryFiles: + - ^.bai + - id: reference + type: File + inputBinding: + position: 3 + prefix: '--reference' + doc: Reference sequence file + secondaryFiles: + - .fai + - ^.dict + - id: output_file_name + type: string? + doc: Output file name. Not Required + - id: output_file_name_metrics + type: string? + doc: Output file name for metrics file. Not Required + - id: probability + type: float? + inputBinding: + position: 4 + prefix: '--PROBABILITY' + doc: 'The probability of keeping any individual read, between 0 and 1.' + - id: random_seed + type: float? + inputBinding: + position: 4 + prefix: '--RANDOM_SEED' + doc: >- + Random seed used for deterministic results. Setting to null will cause + multiple invocations to produce different results. + - id: strategy + type: string? + inputBinding: + position: 4 + prefix: '--STRATEGY' + doc: >- + The --STRATEGY argument is an enumerated type (Strategy), which can have + one of the following values: + + + HighAccuracy + + ConstantMemory + + Chained + + default Strategy ConstantMemory + - id: arguments_file + type: + - 'null' + - type: array + items: File + inputBinding: + position: 0 + prefix: '--arguments_file' + - id: cloud-index-prefetch-buffer + type: int? + inputBinding: + position: 10 + prefix: '--cloud-index-prefetch-buffer' + - id: cloud_prefetch_buffer + type: int? + inputBinding: + position: 10 + prefix: '--cloud-prefetch-buffer' + - id: create_output_bam_index + type: boolean? + inputBinding: + position: 10 + prefix: '--create-output-bam-index' + - id: create_output_bam_md5 + type: boolean? + inputBinding: + position: 10 + prefix: '--create-output-bam-md5' + - id: disable_bam_index_caching + type: boolean? + inputBinding: + position: 10 + prefix: '--disable-bam-index-caching' + - id: disable_read_filter + type: + - 'null' + - type: array + items: string + inputBinding: + prefix: '--disable-read-filter' + inputBinding: + position: 10 + doc: Read filters to be disabled before analysis + - id: disable_sequence_dictionary_validation + type: boolean? + inputBinding: + position: 10 + prefix: '--disable-sequence-dictionary-validation' + - id: exclude_intervals + type: string? + inputBinding: + position: 10 + prefix: '--exclude-intervals' + - id: gatk_config_file + type: File? + inputBinding: + position: 10 + prefix: '--gatk-config-file' + - id: gcs_max_retries + type: int? + inputBinding: + position: 10 + prefix: '--gcs-max-retries' + - id: gcs_project_for_requester_pays + type: string? + inputBinding: + position: 10 + prefix: '--gcs-project-for-requester-pays' + - id: QUIET + type: boolean? + inputBinding: + position: 10 + prefix: '--QUIET' + - id: read_filter + type: + - 'null' + - type: array + items: string + inputBinding: + prefix: '--read-filter' + inputBinding: + position: 10 + - id: read_index + type: string? + inputBinding: + position: 10 + prefix: '--read-index' + - id: seconds_between_progress_updates + type: float? + inputBinding: + position: 10 + prefix: '--seconds-between-progress-updates' + - id: lenient + type: boolean? + inputBinding: + position: 6 + prefix: '--lenient' + - id: number_of_threads + type: int? + - id: memory_per_job + type: int? + - id: memory_overhead + type: int? + - id: temporary_directory + type: string? + doc: 'Default value: null.' +outputs: + - id: gatk_downsamplesam_output_bam + type: File + outputBinding: + glob: |- + ${ + if(inputs.output_file_name){ + return inputs.output_file_name + } else { + return inputs.input.basename.replace(/.bam/, '_downsamplesam.bam') + } + } + secondaryFiles: + - ^.bai + - id: gatk_downsamplesam_output_metrics + type: File + outputBinding: + glob: |- + ${ + if(inputs.output_metrics_file_name){ + return inputs.output_metrics_file_name + } else { + return inputs.input.basename.replace(/.bam/, '_downsamplesam.metrics') + } + } +label: gatk_downsample_sam_4.1.8.1 +arguments: + - position: 0 + prefix: '--java-options' + valueFrom: |- + ${ + if(inputs.memory_per_job && inputs.memory_overhead){ + if(inputs.memory_per_job % 1000 == 0){ + return "-Xmx" + (inputs.memory_per_job/1000).toString() + "G" + } else { + return "-Xmx" + Math.floor((inputs.memory_per_job/1000)).toString() + "G" + } + } else if (inputs.memory_per_job && !inputs.memory_overhead){ + if(inputs.memory_per_job % 1000 == 0) { + return "-Xmx" + (inputs.memory_per_job/1000).toString() + "G" + } else { + return "-Xmx" + Math.floor((inputs.memory_per_job/1000)).toString() + "G" + } + } else if(!inputs.memory_per_job && inputs.memory_overhead){ + return "-Xmx12G" + } else { + return "-Xmx12G" + } + } + - position: 2 + prefix: '--tmp-dir' + valueFrom: |- + ${ + if(inputs.temporary_directory) + return inputs.temporary_directory; + return runtime.tmpdir + } + - position: 2 + prefix: '--output' + valueFrom: |- + ${ + if(inputs.output_file_name){ + return inputs.output_file_name + } else { + return inputs.input.basename.replace(/.bam/, '_downsamplesam.bam') + } + } + - position: 2 + prefix: '--METRICS_FILE' + valueFrom: |- + ${ + if(inputs.output_metrics_file_name){ + return inputs.output_metrics_file_name + } else { + return inputs.input.basename.replace(/.bam/, '_downsamplesam.metrics') + } + } +requirements: + - class: ResourceRequirement + ramMin: 20000 + coresMin: 2 + - class: DockerRequirement + dockerPull: 'ghcr.io/msk-access/gatk:4.1.8.1' + - class: InlineJavascriptRequirement +'dct:contributor': + - class: 'foaf:Organization' + 'foaf:member': + - class: 'foaf:Person' + 'foaf:mbox': 'mailto:shahr2@mskcc.org' + 'foaf:name': Ronak Shah + 'foaf:name': Memorial Sloan Kettering Cancer Center +'dct:creator': + - class: 'foaf:Organization' + 'foaf:member': + - class: 'foaf:Person' + 'foaf:mbox': 'mailto:shahr2@mskcc.org' + 'foaf:name': Ronak Shah + 'foaf:name': Memorial Sloan Kettering Cancer Center From ef4061f2df656a05cec0a99a7d03525b1c86e9db Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 23 Aug 2021 20:32:10 -0400 Subject: [PATCH 2/8] Remove extra options --- gatk_downsamplesam_4.1.8.1/example_inputs.yml | 20 ++---- .../gatk_downsamplesam_4.1.8.1.cwl | 71 +------------------ 2 files changed, 7 insertions(+), 84 deletions(-) diff --git a/gatk_downsamplesam_4.1.8.1/example_inputs.yml b/gatk_downsamplesam_4.1.8.1/example_inputs.yml index dda5b747..8ea893b7 100644 --- a/gatk_downsamplesam_4.1.8.1/example_inputs.yml +++ b/gatk_downsamplesam_4.1.8.1/example_inputs.yml @@ -1,17 +1,10 @@ QUIET: null arguments_file: null -cloud-index-prefetch-buffer: null -cloud_prefetch_buffer: null create_output_bam_index: null create_output_bam_md5: null -disable_bam_index_caching: null -disable_read_filter: null -disable_sequence_dictionary_validation: null -exclude_intervals: null -gatk_config_file: null -gcs_max_retries: null -gcs_project_for_requester_pays: null -input: null +input: + class: File + path: input.bam lenient: null memory_overhead: null memory_per_job: null @@ -20,10 +13,9 @@ output_file_name: null output_file_name_metrics: null probability: null random_seed: null -read_filter: null -read_index: null -reference: null -seconds_between_progress_updates: null +reference: + class: File + path: reference.fasta strategy: null temporary_directory: null diff --git a/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl b/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl index d235bc0e..af86c37e 100644 --- a/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl +++ b/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl @@ -40,7 +40,7 @@ inputs: prefix: '--PROBABILITY' doc: 'The probability of keeping any individual read, between 0 and 1.' - id: random_seed - type: float? + type: int? inputBinding: position: 4 prefix: '--RANDOM_SEED' @@ -72,16 +72,6 @@ inputs: inputBinding: position: 0 prefix: '--arguments_file' - - id: cloud-index-prefetch-buffer - type: int? - inputBinding: - position: 10 - prefix: '--cloud-index-prefetch-buffer' - - id: cloud_prefetch_buffer - type: int? - inputBinding: - position: 10 - prefix: '--cloud-prefetch-buffer' - id: create_output_bam_index type: boolean? inputBinding: @@ -92,70 +82,11 @@ inputs: inputBinding: position: 10 prefix: '--create-output-bam-md5' - - id: disable_bam_index_caching - type: boolean? - inputBinding: - position: 10 - prefix: '--disable-bam-index-caching' - - id: disable_read_filter - type: - - 'null' - - type: array - items: string - inputBinding: - prefix: '--disable-read-filter' - inputBinding: - position: 10 - doc: Read filters to be disabled before analysis - - id: disable_sequence_dictionary_validation - type: boolean? - inputBinding: - position: 10 - prefix: '--disable-sequence-dictionary-validation' - - id: exclude_intervals - type: string? - inputBinding: - position: 10 - prefix: '--exclude-intervals' - - id: gatk_config_file - type: File? - inputBinding: - position: 10 - prefix: '--gatk-config-file' - - id: gcs_max_retries - type: int? - inputBinding: - position: 10 - prefix: '--gcs-max-retries' - - id: gcs_project_for_requester_pays - type: string? - inputBinding: - position: 10 - prefix: '--gcs-project-for-requester-pays' - id: QUIET type: boolean? inputBinding: position: 10 prefix: '--QUIET' - - id: read_filter - type: - - 'null' - - type: array - items: string - inputBinding: - prefix: '--read-filter' - inputBinding: - position: 10 - - id: read_index - type: string? - inputBinding: - position: 10 - prefix: '--read-index' - - id: seconds_between_progress_updates - type: float? - inputBinding: - position: 10 - prefix: '--seconds-between-progress-updates' - id: lenient type: boolean? inputBinding: From b95a0ebee5d4289ce9a0998bed40c3c8c4847c30 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 23 Aug 2021 20:48:20 -0400 Subject: [PATCH 3/8] Update gatk_downsamplesam_4.1.8.1.cwl --- .../gatk_downsamplesam_4.1.8.1.cwl | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl b/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl index af86c37e..be8b0d37 100644 --- a/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl +++ b/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl @@ -76,22 +76,22 @@ inputs: type: boolean? inputBinding: position: 10 - prefix: '--create-output-bam-index' + prefix: '--CREATE_INDEX' - id: create_output_bam_md5 type: boolean? inputBinding: position: 10 - prefix: '--create-output-bam-md5' + prefix: '--CREATE_MD5_FILE' - id: QUIET type: boolean? inputBinding: position: 10 prefix: '--QUIET' - - id: lenient - type: boolean? + - id: "validation_stringency" + type: string? inputBinding: position: 6 - prefix: '--lenient' + prefix: '--VALIDATION_STRINGENCY' - id: number_of_threads type: int? - id: memory_per_job @@ -151,7 +151,7 @@ arguments: } } - position: 2 - prefix: '--tmp-dir' + prefix: '--TMP_DIR' valueFrom: |- ${ if(inputs.temporary_directory) @@ -159,7 +159,7 @@ arguments: return runtime.tmpdir } - position: 2 - prefix: '--output' + prefix: '--OUTPUT' valueFrom: |- ${ if(inputs.output_file_name){ From 765859ecf14f6fc57f7abd76f1c6f9aebc263e95 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 23 Aug 2021 20:50:32 -0400 Subject: [PATCH 4/8] Update gatk_downsamplesam_4.1.8.1.cwl --- gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl b/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl index be8b0d37..cde32448 100644 --- a/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl +++ b/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl @@ -14,7 +14,7 @@ inputs: type: File inputBinding: position: 3 - prefix: '--input' + prefix: '--INPUT' doc: BAM/SAM file containing reads secondaryFiles: - ^.bai @@ -22,7 +22,7 @@ inputs: type: File inputBinding: position: 3 - prefix: '--reference' + prefix: '--REFERENCE' doc: Reference sequence file secondaryFiles: - .fai From e89be7487d6582a77aed5a3f1a48ed2d5c4e5552 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 23 Aug 2021 20:52:25 -0400 Subject: [PATCH 5/8] Update gatk_downsamplesam_4.1.8.1.cwl --- gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl b/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl index cde32448..42dee34c 100644 --- a/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl +++ b/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl @@ -22,7 +22,7 @@ inputs: type: File inputBinding: position: 3 - prefix: '--REFERENCE' + prefix: '--REFERENCE_SEQUENCE' doc: Reference sequence file secondaryFiles: - .fai From 3d9bcbf80dc6a82d7fc233c385f110ddac197096 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 23 Aug 2021 21:47:20 -0400 Subject: [PATCH 6/8] Update gatk_downsamplesam_4.1.8.1.cwl --- gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl b/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl index 42dee34c..b4078135 100644 --- a/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl +++ b/gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl @@ -30,7 +30,7 @@ inputs: - id: output_file_name type: string? doc: Output file name. Not Required - - id: output_file_name_metrics + - id: output_metrics_file_name type: string? doc: Output file name for metrics file. Not Required - id: probability From b550dfa7e7ce4c3e31598f429d07853188717a36 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 22 Nov 2021 14:48:36 -0500 Subject: [PATCH 7/8] Adding length_limit option --- fastp_0.20.1/fastp_0.20.1.cwl | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/fastp_0.20.1/fastp_0.20.1.cwl b/fastp_0.20.1/fastp_0.20.1.cwl index b454079f..0610585d 100644 --- a/fastp_0.20.1/fastp_0.20.1.cwl +++ b/fastp_0.20.1/fastp_0.20.1.cwl @@ -93,6 +93,13 @@ inputs: prefix: '--length_required' doc: | reads shorter than length_required will be discarded, default is 15. + - id: maximum_read_length + type: int? + inputBinding: + position: 0 + prefix: '--length_limit' + doc: | + reads longer than length_limit will be discarded, default 0 means no limitation. - default: fastp.json id: json_output_path type: string From bf8850f232acd0abea93b6d0c65ec5b5e3ae2b47 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 22 Nov 2021 14:55:59 -0500 Subject: [PATCH 8/8] Modifying versions --- __init__.py | 2 +- cwl_commandlinetools/__init__.py | 2 +- setup.cfg | 2 +- setup.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/__init__.py b/__init__.py index 687dc425..d62ed77c 100644 --- a/__init__.py +++ b/__init__.py @@ -4,4 +4,4 @@ __author__ = """msk-access""" __email__ = 'msk.access@gmail.com' -__version__ = '0.6.3' +__version__ = '1.1.1' diff --git a/cwl_commandlinetools/__init__.py b/cwl_commandlinetools/__init__.py index 9fc9a3c6..d62ed77c 100644 --- a/cwl_commandlinetools/__init__.py +++ b/cwl_commandlinetools/__init__.py @@ -4,4 +4,4 @@ __author__ = """msk-access""" __email__ = 'msk.access@gmail.com' -__version__ = '1.0.0' +__version__ = '1.1.1' diff --git a/setup.cfg b/setup.cfg index fd44fded..b734aaf6 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.0.0 +current_version = 1.1.1 commit = True tag = True diff --git a/setup.py b/setup.py index 79f00425..b10c17b2 100644 --- a/setup.py +++ b/setup.py @@ -38,6 +38,6 @@ test_suite='tests', tests_require=test_requirements, url='https://github.com/msk-access/cwl-commandlinetools', - version='1.0.0', + version='1.1.1', zip_safe=False, )