From cad6c7d781e419591338f9431c93807019d5ca49 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Mon, 29 Jun 2020 10:37:53 +0100 Subject: [PATCH] luslab-umitools | Corrections to hash checking --- tools/umi_tools/test/main.nf | 7 ++----- tools/umi_tools/test/output/sample1.dedup.bam | Bin 19574 -> 0 bytes .../umi_tools/test/output/sample1.dedup.bam.bai | Bin 1128 -> 0 bytes tools/umi_tools/test/output/sample2.dedup.bam | Bin 4198 -> 0 bytes .../umi_tools/test/output/sample2.dedup.bam.bai | Bin 1176 -> 0 bytes tools/umi_tools/test/output/sample3.dedup.bam | Bin 5063 -> 0 bytes .../umi_tools/test/output/sample3.dedup.bam.bai | Bin 1320 -> 0 bytes tools/umi_tools/test/output/sample4.dedup.bam | Bin 14047 -> 0 bytes .../umi_tools/test/output/sample4.dedup.bam.bai | Bin 1032 -> 0 bytes tools/umi_tools/test/output/sample5.dedup.bam | Bin 6649 -> 0 bytes .../umi_tools/test/output/sample5.dedup.bam.bai | Bin 1224 -> 0 bytes tools/umi_tools/test/output/sample6.dedup.bam | Bin 6173 -> 0 bytes .../umi_tools/test/output/sample6.dedup.bam.bai | Bin 1344 -> 0 bytes 13 files changed, 2 insertions(+), 5 deletions(-) delete mode 100644 tools/umi_tools/test/output/sample1.dedup.bam delete mode 100644 tools/umi_tools/test/output/sample1.dedup.bam.bai delete mode 100644 tools/umi_tools/test/output/sample2.dedup.bam delete mode 100644 tools/umi_tools/test/output/sample2.dedup.bam.bai delete mode 100644 tools/umi_tools/test/output/sample3.dedup.bam delete mode 100644 tools/umi_tools/test/output/sample3.dedup.bam.bai delete mode 100644 tools/umi_tools/test/output/sample4.dedup.bam delete mode 100644 tools/umi_tools/test/output/sample4.dedup.bam.bai delete mode 100644 tools/umi_tools/test/output/sample5.dedup.bam delete mode 100644 tools/umi_tools/test/output/sample5.dedup.bam.bai delete mode 100644 tools/umi_tools/test/output/sample6.dedup.bam delete mode 100644 tools/umi_tools/test/output/sample6.dedup.bam.bai diff --git a/tools/umi_tools/test/main.nf b/tools/umi_tools/test/main.nf index e0bf3cc2..6e40d5e1 100644 --- a/tools/umi_tools/test/main.nf +++ b/tools/umi_tools/test/main.nf @@ -11,7 +11,7 @@ log.info ("Starting tests for umi_tools dedup...") --------------------------------------------------------------------------------------*/ params.umitools_dedup_args = '--umi-separator=":"' -params.verbose = true +params.verbose = false /*------------------------------------------------------------------------------------*/ /* Module inclusions @@ -46,13 +46,10 @@ Channel workflow { // Run dedup umitools_dedup ( ch_bam ) - - // Collect file names and view output - umitools_dedup.out.dedupBam | view } workflow.onComplete { - def proc = "$baseDir/verify-checksum.sh $baseDir/../../../results/umitools/dedup/*.bai $baseDir/output/*.bai".execute() + def proc = "$baseDir/verify-checksum.sh $baseDir/../../../results/umitools/dedup/*.bam $baseDir/output/*.bam".execute() def b = new StringBuffer() proc.consumeProcessErrorStream(b) diff --git 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