From 1a66b421da5ff506daa97d2e665193b2be68ec8e Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 23 Nov 2021 10:56:45 -0500 Subject: [PATCH 1/2] Update for fastp --- command_line_tools | 2 +- uncollapsed_bam_generation.cwl | 16 ++++++++++++++-- 2 files changed, 15 insertions(+), 3 deletions(-) diff --git a/command_line_tools b/command_line_tools index e6e684e..3c3cbdb 160000 --- a/command_line_tools +++ b/command_line_tools @@ -1 +1 @@ -Subproject commit e6e684e12b588d42e33b99aba0777d93dd150429 +Subproject commit 3c3cbdbf59daef7f34114468e127c744fb3a2580 diff --git a/uncollapsed_bam_generation.cwl b/uncollapsed_bam_generation.cwl index 06823bb..9d61ff0 100644 --- a/uncollapsed_bam_generation.cwl +++ b/uncollapsed_bam_generation.cwl @@ -449,10 +449,18 @@ inputs: type: string? 'sbg:x': 0 'sbg:y': 3310.703125 - - id: maximum_read_length + - id: fastp_maximum_read_length type: int? 'sbg:x': 0 'sbg:y': 2135.9375 + - id: fastp_max_len_read1 + type: int? + 'sbg:x': 1773.6907958984375 + 'sbg:y': 3302.252197265625 + - id: fastp_max_len_read2 + type: int? + 'sbg:x': 1686.5479736328125 + 'sbg:y': 3223.680908203125 outputs: - id: gatk_sam_to_fastq_unpaired_fastq outputSource: @@ -600,7 +608,11 @@ steps: - id: minimum_read_length source: fastp_minimum_read_length - id: maximum_read_length - source: maximum_read_length + source: fastp_maximum_read_length + - id: max_len_read1 + source: fastp_max_len_read1 + - id: max_len_read2 + source: fastp_max_len_read2 - id: json_output_path source: fastp_json_output_file_name - id: html_output_path From 06767e67aaa06999dfaf081b4c5e386ac21213fd Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 23 Nov 2021 10:59:29 -0500 Subject: [PATCH 2/2] =?UTF-8?q?Bump=20version:=201.1.0=20=E2=86=92=201.2.0?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- setup.cfg | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 751dfae..2283863 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.1.0 +current_version = 1.2.0 commit = True tag = True diff --git a/setup.py b/setup.py index 0eed26c..b0209b9 100644 --- a/setup.py +++ b/setup.py @@ -36,6 +36,6 @@ test_suite='tests', tests_require=test_requirements, url='https://github.com/msk-access/uncollapsed_bam_generation', - version='1.1.0', + version='1.2.0', zip_safe=False, )