common-workflow-language/cwltool: 3.1.20231114134824

<h2>What's Changed</h2> <ul> <li>gh-actions: need newer setuptools to run setuptools_scm by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1932</li> <li>Update ruamel-yaml requirement from <0.18,>=0.16.0 to >=0.16.0,<0.19 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1934</li> <li>software dependencies: allow newer versions of galaxy-tool-util by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1936</li> <li>skip cwl-utils 0.30 by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1941</li> <li>Update black requirement from ~=23.10 to ~=23.11 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1939</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231020140205...3.1.20231114134824</p&gt

common-workflow-language/cwltool: 3.1.20231020140205

<h2>What's Changed</h2> <ul> <li>fix the pickling error for IO objects by @ndonyapour in https://github.com/common-workflow-language/cwltool/pull/1929</li> <li>gh-actions: record version before building container to publish to quay.io by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1931</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231020113452...3.1.20231020140205</p&gt

common-workflow-language/cwltool: 3.1.20240112164112

<h2>What's Changed</h2> <ul> <li>Fix fast container job hangs by @kuanyili in https://github.com/common-workflow-language/cwltool/pull/1962</li> <li>Permit calling cwltool.main with preparsed args only even with provenance by @davidjsherman in https://github.com/common-workflow-language/cwltool/pull/1964</li> <li>rename singularity image by @misterbrandonwalker in https://github.com/common-workflow-language/cwltool/pull/1956</li> <li>remove galaxy-tool-util from build dependency by @jfennick in https://github.com/common-workflow-language/cwltool/pull/1955</li> <li>Added new test on loop by @LanderOtto in https://github.com/common-workflow-language/cwltool/pull/1965</li> </ul> <h3>Deps</h3> <ul> <li>Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1952</li> <li>Update black requirement from ~=23.11 to ~=23.12 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1957</li> <li>Bump github/codeql-action from 2 to 3 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1958</li> <li>Bump actions/upload-artifact from 3 to 4 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1959</li> <li>Bump mypy from 1.7.1 to 1.8.0 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1960</li> </ul> <h2>New Contributors</h2> <ul> <li>@kuanyili made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1962</li> <li>@LanderOtto made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1965</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231207110929...3.1.20240112164112</p&gt

common-workflow-language/cwltool: 3.1.20231020113452

<h2>What's Changed</h2> <ul> <li>temporarily downgrade galaxy-tool-util to workaround issue with newer conda by @mr-c in https://github.com/common-workflow-language /cwltool/pull/1930</li> </ul> <h3>Deps</h3> <ul> <li>Bump mypy from 1.6.0 to 1.6.1 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1927</li> <li>Update black requirement from ~=23.9 to ~=23.10 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1926</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231016170136...3.1.20231020113452</p&gt

bcbio/bcbio-nextgen:

Fix vcf header bug: T/N SAMPLE lines are back - needed for import to SolveBio add strandedness: auto for -l A option in salmon report 10x more peaks in CHIP/ATAC-seq - use 0.05 qvalue fix misleading RNA-seq duplicated reads statistics: thanks @sib-bcf reorganize conda environments snpEff 5.0 strandedness: auto document WGBS pipeline steps make --local an option, not default in bismark alignment - too slow bcbioRNASeq update to 0.3.44 pureCN update to 2.0.1 octopus update to 0.7.