Add option to DemuxFastqs to filter on the internal control flag in the header comment #714
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nh13
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Sep 20, 2021
| @@ -293,9 +293,13 @@ object DemuxFastqs { | |||
| | | |||
| |`--fastq-skip-read-numbers=true --fastq-include-sample-barcodes=true --illumina-file-names=true` | |||
| | | |||
| |To output reads with a passing filter flag, use: | |||
| |To output reads with a passing filter flag, as encoded in the <is filtered> field in the header comment, use: | |||
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Adding backticks, since the usage is parsed as markdown, which is really nice.
Suggested change
| |To output reads with a passing filter flag, as encoded in the <is filtered> field in the header comment, use: | |
| |To output reads with a passing filter flag, as encoded in the `<is filtered>` field in the header comment, use: |
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Also, I think you're mixing up PRs, as I think I asked for this in the other PR: #713 (comment)
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Codecov Report
@@ Coverage Diff @@
## master #714 +/- ##
=======================================
Coverage 95.39% 95.39%
=======================================
Files 114 114
Lines 6601 6606 +5
Branches 457 440 -17
=======================================
+ Hits 6297 6302 +5
Misses 304 304
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nh13
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Sep 22, 2021
tfenne
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Sep 22, 2021
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nh13
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Sep 24, 2021
nh13
requested changes
Sep 24, 2021
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| fastqStandards = this.fastqStandards, | ||
| skipFailingReads = this.skipFailingReads | ||
| skipFailingReads = this.skipFailingReads, | ||
| omitControlReads = this.omitControlReads |
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| sources = sources, | ||
| demultiplexer = demultiplexer, | ||
| threads = threads, | ||
| skipFailingReads = this.skipFailingReads, | ||
| omitControlReads = this.omitControlReads | ||
| ) |
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Suggested change
| sources = sources, | |
| demultiplexer = demultiplexer, | |
| threads = threads, | |
| skipFailingReads = this.skipFailingReads, | |
| omitControlReads = this.omitControlReads | |
| ) | |
| sources = sources, | |
| demultiplexer = demultiplexer, | |
| threads = threads, | |
| skipFailingReads = this.skipFailingReads, | |
| omitControlReads = this.omitControlReads | |
| ) |
tfenne
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