{"action":"created","issue":{"url":"https://api.github.com/repos/mskcc/process_fastq/issues/29","repository_url":"https://api.github.com/repos/mskcc/process_fastq","labels_url":"https://api.github.com/repos/mskcc/process_fastq/issues/29/labels{/name}","comments_url":"https://api.github.com/repos/mskcc/process_fastq/issues/29/comments","events_url":"https://api.github.com/repos/mskcc/process_fastq/issues/29/events","html_url":"https://github.com/mskcc/process_fastq/pull/29","id":527705360,"node_id":"MDExOlB1bGxSZXF1ZXN0MzQ0OTEyMTU3","number":29,"title":"Update cutadapt to 2.7","user":{"login":"pyup-bot","id":16239342,"node_id":"MDQ6VXNlcjE2MjM5MzQy","avatar_url":"https://avatars0.githubusercontent.com/u/16239342?v=4","gravatar_id":"","url":"https://api.github.com/users/pyup-bot","html_url":"https://github.com/pyup-bot","followers_url":"https://api.github.com/users/pyup-bot/followers","following_url":"https://api.github.com/users/pyup-bot/following{/other_user}","gists_url":"https://api.github.com/users/pyup-bot/gists{/gist_id}","starred_url":"https://api.github.com/users/pyup-bot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pyup-bot/subscriptions","organizations_url":"https://api.github.com/users/pyup-bot/orgs","repos_url":"https://api.github.com/users/pyup-bot/repos","events_url":"https://api.github.com/users/pyup-bot/events{/privacy}","received_events_url":"https://api.github.com/users/pyup-bot/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2019-11-24T14:23:13Z","updated_at":"2020-01-13T13:46:41Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/mskcc/process_fastq/pulls/29","html_url":"https://github.com/mskcc/process_fastq/pull/29","diff_url":"https://github.com/mskcc/process_fastq/pull/29.diff","patch_url":"https://github.com/mskcc/process_fastq/pull/29.patch"},"body":"\nThis PR updates [cutadapt](https://pypi.org/project/cutadapt) from **2.4** to **2.7**.\n\n\n\n<details>\n  <summary>Changelog</summary>\n  \n  \n   ### 2.7\n   ```\n   -----------------\n\n* :issue:`427`: Multicore is now supported even when using ``--info-file``,\n  ``--rest-file`` or ``--wildcard-file``. The only remaining feature that\n  still does not work with multicore is now demultiplexing.\n* :issue:`290`: When running on a single core, Cutadapt no longer spawns\n  external ``pigz`` processes for writing gzip-compressed files. This is a first\n  step towards ensuring that using ``--cores=n`` uses only at most *n* CPU\n  cores.\n* This release adds support for Python 3.8.\n   ```\n   \n  \n  \n   ### 2.6\n   ```\n   -----------------\n\n* :issue:`395`: Do not show animated progress when ``--quiet`` is used.\n* :issue:`399`: When two adapters align to a read equally well (in terms\n  of the number of matches), prefer the alignment that has fewer errors.\n* :issue:`401` Give priority to adapters given earlier on the command\n  line. Previously, the priority was: All 3&#39; adapters, all 5&#39; adapters,\n  all anywhere adapters. In rare cases this could lead to different results.\n* :issue:`404`: Fix an issue preventing Cutadapt from being used on Windows.\n* This release no longer supports Python 3.4 (which has reached end of life).\n   ```\n   \n  \n  \n   ### 2.5\n   ```\n   -----------------\n\n* :issue:`391`: Multicore is now supported even when using\n  ``--untrimmed-output``, ``--too-short-output``, ``--too-long-output``\n  or the corresponding ``...-paired-output`` options.\n* :issue:`393`: Using ``--info-file`` no longer crashes when processing\n  paired-end data. However, the info file itself will only contain results\n  for R1.\n* :issue:`394`: Options ``-e``/``--no-indels``/``-O`` were ignored for\n  linked adapters\n* :issue:`320`: When a “Too many open files” error occurs during\n  demultiplexing, Cutadapt can now automatically raise the limit and\n  re-try if the limit is a “soft” limit.\n   ```\n   \n  \n</details>\n\n\n \n\n<details>\n  <summary>Links</summary>\n  \n  - PyPI: https://pypi.org/project/cutadapt\n  - Changelog: https://pyup.io/changelogs/cutadapt/\n  - Docs: https://cutadapt.readthedocs.io/\n</details>\n\n"},"comment":{"url":"https://api.github.com/repos/mskcc/process_fastq/issues/comments/573670476","html_url":"https://github.com/mskcc/process_fastq/pull/29#issuecomment-573670476","issue_url":"https://api.github.com/repos/mskcc/process_fastq/issues/29","id":573670476,"node_id":"MDEyOklzc3VlQ29tbWVudDU3MzY3MDQ3Ng==","user":{"login":"pyup-bot","id":16239342,"node_id":"MDQ6VXNlcjE2MjM5MzQy","avatar_url":"https://avatars0.githubusercontent.com/u/16239342?v=4","gravatar_id":"","url":"https://api.github.com/users/pyup-bot","html_url":"https://github.com/pyup-bot","followers_url":"https://api.github.com/users/pyup-bot/followers","following_url":"https://api.github.com/users/pyup-bot/following{/other_user}","gists_url":"https://api.github.com/users/pyup-bot/gists{/gist_id}","starred_url":"https://api.github.com/users/pyup-bot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pyup-bot/subscriptions","organizations_url":"https://api.github.com/users/pyup-bot/orgs","repos_url":"https://api.github.com/users/pyup-bot/repos","events_url":"https://api.github.com/users/pyup-bot/events{/privacy}","received_events_url":"https://api.github.com/users/pyup-bot/received_events","type":"User","site_admin":false},"created_at":"2020-01-13T13:46:41Z","updated_at":"2020-01-13T13:46:41Z","author_association":"CONTRIBUTOR","body":"Closing this in favor of #40"}}
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