diff --git a/software/samtools/stats/test/input/test.paired_end.sorted.bam b/software/samtools/stats/test/input/test.paired_end.sorted.bam deleted file mode 120000 index af606d91..00000000 --- a/software/samtools/stats/test/input/test.paired_end.sorted.bam +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/data/bam/test.paired_end.sorted.bam \ No newline at end of file diff --git a/software/samtools/stats/test/input/test.paired_end.sorted.bam.bai b/software/samtools/stats/test/input/test.paired_end.sorted.bam.bai deleted file mode 120000 index 61a71557..00000000 --- a/software/samtools/stats/test/input/test.paired_end.sorted.bam.bai +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/data/bam/test.paired_end.sorted.bam.bai \ No newline at end of file diff --git a/software/samtools/stats/test/main.nf b/software/samtools/stats/test/main.nf deleted file mode 100755 index a3388303..00000000 --- a/software/samtools/stats/test/main.nf +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { SAMTOOLS_STATS } from '../main.nf' addParams( options: [:] ) - -workflow test { - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true), - file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ] - - SAMTOOLS_STATS ( input ) -} - -workflow { - test() -} diff --git a/software/samtools/stats/test/nextflow.config b/software/samtools/stats/test/nextflow.config deleted file mode 100644 index 4149feea..00000000 --- a/software/samtools/stats/test/nextflow.config +++ /dev/null @@ -1,20 +0,0 @@ - -params { - outdir = "output/" - publish_dir_mode = "copy" - enable_conda = false -} - -profiles { - conda { - params.enable_conda = true - } - docker { - docker.enabled = true - docker.runOptions = '-u \$(id -u):\$(id -g)' - } - singularity { - singularity.enabled = true - singularity.autoMounts = true - } -} diff --git a/software/samtools/stats/test/output/samtools/test.paired_end.sorted.bam.stats b/software/samtools/stats/test/output/samtools/test.paired_end.sorted.bam.stats deleted file mode 100644 index 0de94d2f..00000000 --- a/software/samtools/stats/test/output/samtools/test.paired_end.sorted.bam.stats +++ /dev/null @@ -1,1105 +0,0 @@ -# This file was produced by samtools stats (1.10+htslib-1.10.2) and can be plotted using plot-bamstats -# This file contains statistics for all reads. -# The command line was: stats test.paired_end.sorted.bam -# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities -# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) -CHK 8e5d2ba0 549f6ff5 2a9028a0 -# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 20000 -SN filtered sequences: 0 -SN sequences: 20000 -SN is sorted: 1 -SN 1st fragments: 10000 -SN last fragments: 10000 -SN reads mapped: 20000 -SN reads mapped and paired: 20000 # paired-end technology bit set + both mates mapped -SN reads unmapped: 0 -SN reads properly paired: 20000 # proper-pair bit set -SN reads paired: 20000 # paired-end technology bit set -SN reads duplicated: 0 # PCR or optical duplicate bit set -SN reads MQ0: 1262 # mapped and MQ=0 -SN reads QC failed: 0 -SN non-primary alignments: 0 -SN total length: 2000000 # ignores clipping -SN total first fragment length: 1000000 # ignores clipping -SN total last fragment length: 1000000 # ignores clipping -SN bases mapped: 2000000 # ignores clipping -SN bases mapped (cigar): 2000000 # more accurate -SN bases trimmed: 0 -SN bases duplicated: 0 -SN mismatches: 1 # from NM fields -SN error rate: 5.000000e-07 # mismatches / bases mapped (cigar) -SN average length: 100 -SN average first fragment length: 100 -SN average last fragment length: 100 -SN maximum length: 100 -SN maximum first fragment length: 100 -SN maximum last fragment length: 100 -SN average quality: 40.0 -SN insert size average: 233.4 -SN insert size standard deviation: 94.1 -SN inward oriented pairs: 9087 -SN outward oriented pairs: 913 -SN pairs with other orientation: 0 -SN pairs on different chromosomes: 0 -SN percentage of properly paired reads (%): 100.0 -# First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part. -# Columns correspond to qualities and rows to cycles. First column is the cycle number. -FFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -FFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -FFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -FFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -FFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -FFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -FFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -FFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -FFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -FFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -FFQ 11 0 0 0 0 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0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 34 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 48 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 52 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 59 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 61 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 68 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 71 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 72 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 73 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 74 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 77 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 78 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 79 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 81 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 82 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 83 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 86 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 87 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 88 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 89 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 91 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 92 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 93 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 96 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 97 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 98 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 99 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -LFQ 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 -# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. -GCF 7.29 0 -GCF 15.08 3 -GCF 16.58 0 -GCF 18.09 2 -GCF 19.60 1 -GCF 21.11 0 -GCF 22.11 5 -GCF 23.12 6 -GCF 24.12 7 -GCF 25.13 10 -GCF 26.13 14 -GCF 27.14 12 -GCF 28.14 24 -GCF 29.15 26 -GCF 30.65 36 -GCF 32.16 43 -GCF 33.17 53 -GCF 34.17 66 -GCF 35.18 57 -GCF 36.18 63 -GCF 37.19 76 -GCF 38.19 88 -GCF 39.20 108 -GCF 40.20 140 -GCF 41.21 160 -GCF 42.21 183 -GCF 43.22 214 -GCF 44.22 238 -GCF 45.23 297 -GCF 46.23 340 -GCF 47.24 387 -GCF 48.24 490 -GCF 49.25 538 -GCF 50.25 581 -GCF 51.26 597 -GCF 52.26 614 -GCF 53.27 669 -GCF 54.27 645 -GCF 55.28 576 -GCF 56.28 499 -GCF 57.29 488 -GCF 58.29 376 -GCF 59.30 340 -GCF 60.30 238 -GCF 61.31 192 -GCF 62.31 144 -GCF 63.32 102 -GCF 64.32 76 -GCF 65.33 62 -GCF 66.33 22 -GCF 67.34 26 -GCF 68.34 14 -GCF 69.35 6 -GCF 70.85 2 -GCF 72.86 1 -GCF 74.37 0 -GCF 75.88 1 -GCF 77.39 0 -GCF 78.39 1 -# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. -GCL 7.29 0 -GCL 15.08 1 -GCL 16.58 0 -GCL 18.59 1 -GCL 20.10 3 -GCL 21.61 4 -GCL 23.62 5 -GCL 25.13 9 -GCL 26.13 12 -GCL 27.14 15 -GCL 28.14 23 -GCL 29.15 31 -GCL 30.15 33 -GCL 31.16 39 -GCL 32.16 32 -GCL 33.17 59 -GCL 34.17 57 -GCL 35.18 76 -GCL 36.18 77 -GCL 37.19 83 -GCL 38.19 104 -GCL 39.20 117 -GCL 40.20 123 -GCL 41.21 148 -GCL 42.21 152 -GCL 43.22 208 -GCL 44.22 252 -GCL 45.23 280 -GCL 46.23 358 -GCL 47.24 406 -GCL 48.24 455 -GCL 49.25 571 -GCL 50.25 543 -GCL 51.26 623 -GCL 52.26 618 -GCL 53.27 639 -GCL 54.27 653 -GCL 55.28 557 -GCL 56.28 555 -GCL 57.29 458 -GCL 58.29 398 -GCL 59.30 313 -GCL 60.30 252 -GCL 61.31 199 -GCL 62.31 130 -GCL 63.32 98 -GCL 64.32 79 -GCL 65.33 56 -GCL 66.33 36 -GCL 67.34 24 -GCL 68.34 9 -GCL 69.35 8 -GCL 70.35 4 -GCL 71.36 1 -GCL 72.36 2 -GCL 73.37 1 -# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] -GCC 1 24.39 25.20 25.94 24.46 0.00 0.00 -GCC 2 24.56 24.86 25.73 24.86 0.00 0.00 -GCC 3 24.42 25.51 25.64 24.43 0.00 0.00 -GCC 4 25.19 25.35 24.91 24.55 0.00 0.00 -GCC 5 25.01 25.31 25.20 24.48 0.00 0.00 -GCC 6 24.82 25.40 25.16 24.62 0.00 0.00 -GCC 7 24.18 25.38 26.57 23.88 0.00 0.00 -GCC 8 24.39 25.97 25.07 24.57 0.00 0.00 -GCC 9 24.13 26.01 25.25 24.61 0.00 0.00 -GCC 10 24.59 24.96 25.46 24.98 0.00 0.00 -GCC 11 24.73 25.34 25.30 24.64 0.00 0.00 -GCC 12 24.85 25.85 25.11 24.20 0.00 0.00 -GCC 13 25.25 24.68 25.88 24.18 0.00 0.00 -GCC 14 24.20 25.52 25.98 24.31 0.00 0.00 -GCC 15 24.73 25.58 25.38 24.32 0.00 0.00 -GCC 16 25.11 25.61 25.04 24.25 0.00 0.00 -GCC 17 24.63 25.30 25.43 24.64 0.00 0.00 -GCC 18 23.91 25.69 25.55 24.86 0.00 0.00 -GCC 19 24.45 25.36 25.32 24.86 0.00 0.00 -GCC 20 24.23 25.50 25.18 25.09 0.00 0.00 -GCC 21 25.32 25.07 24.76 24.85 0.00 0.00 -GCC 22 24.73 25.41 24.79 25.07 0.00 0.00 -GCC 23 24.57 25.70 25.55 24.18 0.00 0.00 -GCC 24 24.18 25.91 25.64 24.27 0.00 0.00 -GCC 25 23.95 25.23 25.78 25.04 0.00 0.00 -GCC 26 24.84 25.20 25.23 24.73 0.00 0.00 -GCC 27 24.25 25.88 25.27 24.59 0.00 0.00 -GCC 28 24.86 25.67 25.05 24.43 0.00 0.00 -GCC 29 24.71 25.32 25.55 24.41 0.00 0.00 -GCC 30 24.93 25.47 24.93 24.67 0.00 0.00 -GCC 31 24.43 25.41 25.72 24.45 0.00 0.00 -GCC 32 24.48 25.72 25.11 24.70 0.00 0.00 -GCC 33 24.18 25.95 25.20 24.66 0.00 0.00 -GCC 34 24.93 24.84 25.78 24.46 0.00 0.00 -GCC 35 24.31 26.11 25.29 24.30 0.00 0.00 -GCC 36 24.07 25.66 25.56 24.70 0.00 0.00 -GCC 37 24.75 25.04 26.09 24.12 0.00 0.00 -GCC 38 24.68 26.14 24.70 24.49 0.00 0.00 -GCC 39 24.16 25.68 25.14 25.00 0.00 0.00 -GCC 40 24.53 25.16 25.43 24.89 0.00 0.00 -GCC 41 24.46 25.48 24.91 25.16 0.00 0.00 -GCC 42 24.28 26.01 24.86 24.84 0.00 0.00 -GCC 43 24.73 25.66 25.05 24.57 0.00 0.00 -GCC 44 24.98 24.82 25.46 24.73 0.00 0.00 -GCC 45 24.65 25.61 25.43 24.30 0.00 0.00 -GCC 46 24.19 25.32 25.38 25.11 0.00 0.00 -GCC 47 24.89 24.61 25.52 24.98 0.00 0.00 -GCC 48 24.65 25.48 25.20 24.67 0.00 0.00 -GCC 49 25.23 25.59 24.48 24.70 0.00 0.00 -GCC 50 24.63 25.23 25.45 24.68 0.00 0.00 -GCC 51 24.73 25.61 25.44 24.21 0.00 0.00 -GCC 52 24.50 25.30 25.48 24.71 0.00 0.00 -GCC 53 25.05 25.48 25.13 24.35 0.00 0.00 -GCC 54 24.36 25.73 25.39 24.52 0.00 0.00 -GCC 55 24.45 25.20 25.51 24.83 0.00 0.00 -GCC 56 24.00 25.68 25.90 24.43 0.00 0.00 -GCC 57 24.45 25.07 25.32 25.16 0.00 0.00 -GCC 58 24.53 25.56 25.10 24.81 0.00 0.00 -GCC 59 24.37 25.80 25.41 24.43 0.00 0.00 -GCC 60 24.62 25.36 25.37 24.66 0.00 0.00 -GCC 61 24.32 25.51 25.51 24.66 0.00 0.00 -GCC 62 25.02 25.20 25.34 24.43 0.00 0.00 -GCC 63 24.50 25.11 25.57 24.81 0.00 0.00 -GCC 64 24.84 25.41 25.54 24.21 0.00 0.00 -GCC 65 24.79 25.61 25.65 23.95 0.00 0.00 -GCC 66 24.46 24.98 25.62 24.95 0.00 0.00 -GCC 67 24.73 25.04 25.40 24.83 0.00 0.00 -GCC 68 24.39 25.18 25.50 24.94 0.00 0.00 -GCC 69 24.69 25.15 25.35 24.82 0.01 0.00 -GCC 70 24.38 25.48 25.51 24.63 0.00 0.00 -GCC 71 24.26 26.12 25.64 23.98 0.00 0.00 -GCC 72 24.79 25.40 25.32 24.50 0.00 0.00 -GCC 73 25.04 25.18 25.49 24.29 0.00 0.00 -GCC 74 25.16 25.43 24.77 24.64 0.00 0.00 -GCC 75 24.48 25.64 25.19 24.69 0.00 0.00 -GCC 76 24.39 24.95 25.68 24.98 0.00 0.00 -GCC 77 24.81 25.21 25.05 24.92 0.00 0.00 -GCC 78 24.50 25.95 25.48 24.05 0.00 0.00 -GCC 79 24.91 25.66 25.27 24.16 0.00 0.00 -GCC 80 24.43 25.88 25.43 24.26 0.00 0.00 -GCC 81 25.08 25.70 25.36 23.87 0.00 0.00 -GCC 82 23.93 25.97 25.24 24.86 0.00 0.00 -GCC 83 24.87 25.39 25.43 24.32 0.00 0.00 -GCC 84 25.00 25.55 25.18 24.27 0.00 0.00 -GCC 85 24.77 25.00 25.20 25.04 0.00 0.00 -GCC 86 24.21 25.52 25.04 25.23 0.00 0.00 -GCC 87 24.81 25.46 25.36 24.37 0.00 0.00 -GCC 88 25.01 25.44 25.60 23.95 0.00 0.00 -GCC 89 24.58 25.77 25.14 24.52 0.00 0.00 -GCC 90 24.50 25.50 25.47 24.54 0.00 0.00 -GCC 91 25.05 25.23 25.27 24.45 0.00 0.00 -GCC 92 25.06 25.11 25.04 24.79 0.00 0.00 -GCC 93 25.03 25.55 24.81 24.61 0.00 0.00 -GCC 94 24.45 25.79 25.02 24.73 0.00 0.00 -GCC 95 24.86 25.21 25.29 24.64 0.00 0.00 -GCC 96 24.47 25.23 25.61 24.69 0.00 0.00 -GCC 97 24.59 25.02 25.48 24.93 0.00 0.00 -GCC 98 25.10 25.08 25.42 24.40 0.00 0.00 -GCC 99 24.27 25.39 25.83 24.52 0.00 0.00 -GCC 100 23.68 26.05 25.61 24.65 0.00 0.00 -# ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] -FBC 1 24.74 25.02 25.61 24.63 0.00 0.00 -FBC 2 25.50 23.74 25.96 24.80 0.00 0.00 -FBC 3 24.91 25.40 24.96 24.73 0.00 0.00 -FBC 4 25.44 25.36 24.59 24.61 0.00 0.00 -FBC 5 25.33 25.28 25.04 24.35 0.00 0.00 -FBC 6 24.94 25.83 25.25 23.98 0.00 0.00 -FBC 7 24.26 25.58 26.45 23.71 0.00 0.00 -FBC 8 23.87 26.45 25.17 24.51 0.00 0.00 -FBC 9 24.03 26.08 25.70 24.19 0.00 0.00 -FBC 10 24.80 24.80 25.34 25.06 0.00 0.00 -FBC 11 25.03 25.07 24.86 25.04 0.00 0.00 -FBC 12 24.37 25.97 25.25 24.41 0.00 0.00 -FBC 13 25.16 24.85 25.59 24.40 0.00 0.00 -FBC 14 24.27 25.69 25.79 24.25 0.00 0.00 -FBC 15 24.69 25.93 25.62 23.76 0.00 0.00 -FBC 16 24.86 25.94 24.97 24.23 0.00 0.00 -FBC 17 24.38 25.68 25.18 24.76 0.00 0.00 -FBC 18 24.03 25.63 25.90 24.44 0.00 0.00 -FBC 19 24.48 24.89 25.72 24.91 0.00 0.00 -FBC 20 24.06 25.07 25.75 25.12 0.00 0.00 -FBC 21 24.76 25.39 24.40 25.45 0.00 0.00 -FBC 22 25.18 25.02 24.66 25.14 0.00 0.00 -FBC 23 24.54 25.44 25.83 24.19 0.00 0.00 -FBC 24 23.70 26.35 25.59 24.36 0.00 0.00 -FBC 25 23.81 24.86 25.83 25.50 0.00 0.00 -FBC 26 24.57 25.78 25.11 24.54 0.00 0.00 -FBC 27 24.00 25.53 25.80 24.67 0.00 0.00 -FBC 28 24.32 25.76 25.36 24.56 0.00 0.00 -FBC 29 24.57 25.03 26.21 24.19 0.00 0.00 -FBC 30 25.44 25.05 24.70 24.81 0.00 0.00 -FBC 31 24.16 25.28 25.86 24.70 0.00 0.00 -FBC 32 24.45 25.24 25.21 25.10 0.00 0.00 -FBC 33 24.47 26.17 24.98 24.38 0.00 0.00 -FBC 34 24.95 24.47 26.38 24.20 0.00 0.00 -FBC 35 24.46 26.59 24.82 24.13 0.00 0.00 -FBC 36 24.35 25.45 25.70 24.50 0.00 0.00 -FBC 37 24.54 25.05 25.90 24.51 0.00 0.00 -FBC 38 24.82 26.59 24.40 24.19 0.00 0.00 -FBC 39 24.37 25.48 25.59 24.56 0.00 0.00 -FBC 40 24.93 25.40 25.17 24.50 0.00 0.00 -FBC 41 24.60 25.51 24.78 25.11 0.00 0.00 -FBC 42 24.33 26.16 25.04 24.47 0.00 0.00 -FBC 43 25.01 25.57 25.51 23.91 0.00 0.00 -FBC 44 24.57 25.52 25.48 24.43 0.00 0.00 -FBC 45 24.62 25.32 25.59 24.47 0.00 0.00 -FBC 46 24.53 25.40 25.15 24.92 0.00 0.00 -FBC 47 24.59 25.66 24.94 24.81 0.00 0.00 -FBC 48 23.81 25.76 25.33 25.10 0.00 0.00 -FBC 49 25.35 25.70 23.80 25.15 0.00 0.00 -FBC 50 24.53 25.21 25.47 24.79 0.00 0.00 -FBC 51 24.03 25.69 25.92 24.36 0.00 0.00 -FBC 52 23.98 25.01 25.99 25.02 0.00 0.00 -FBC 53 24.46 25.50 25.59 24.45 0.00 0.00 -FBC 54 24.41 25.73 25.45 24.41 0.00 0.00 -FBC 55 25.18 25.19 25.45 24.18 0.00 0.00 -FBC 56 24.18 25.49 25.72 24.61 0.00 0.00 -FBC 57 24.08 25.49 25.41 25.02 0.00 0.00 -FBC 58 24.10 25.35 25.38 25.17 0.00 0.00 -FBC 59 24.58 25.58 25.39 24.45 0.00 0.00 -FBC 60 24.67 25.22 25.47 24.64 0.00 0.00 -FBC 61 24.09 25.56 25.36 24.99 0.00 0.00 -FBC 62 25.20 25.47 25.68 23.65 0.00 0.00 -FBC 63 24.47 25.40 25.28 24.85 0.00 0.00 -FBC 64 24.80 25.45 25.40 24.35 0.00 0.00 -FBC 65 25.08 26.20 24.91 23.81 0.00 0.00 -FBC 66 24.89 24.74 25.37 25.00 0.00 0.00 -FBC 67 25.10 25.13 25.01 24.76 0.00 0.00 -FBC 68 24.73 25.30 25.13 24.84 0.00 0.00 -FBC 69 24.94 25.18 25.20 24.68 0.00 0.00 -FBC 70 24.29 25.21 25.62 24.88 0.00 0.00 -FBC 71 24.21 26.30 25.72 23.77 0.00 0.00 -FBC 72 24.39 25.61 25.34 24.66 0.00 0.00 -FBC 73 25.29 24.55 25.67 24.49 0.00 0.00 -FBC 74 25.66 25.07 24.54 24.73 0.00 0.00 -FBC 75 24.26 26.19 24.81 24.74 0.00 0.00 -FBC 76 24.04 24.89 26.43 24.64 0.00 0.00 -FBC 77 25.01 25.04 25.04 24.91 0.00 0.00 -FBC 78 24.37 26.53 25.05 24.05 0.00 0.00 -FBC 79 24.60 25.35 25.69 24.36 0.00 0.00 -FBC 80 24.90 25.32 25.33 24.45 0.00 0.00 -FBC 81 25.10 26.14 24.64 24.12 0.00 0.00 -FBC 82 23.95 25.90 25.23 24.92 0.00 0.00 -FBC 83 24.73 25.25 25.41 24.61 0.00 0.00 -FBC 84 24.81 25.43 25.68 24.08 0.00 0.00 -FBC 85 24.73 24.72 25.57 24.98 0.00 0.00 -FBC 86 24.12 25.26 25.17 25.45 0.00 0.00 -FBC 87 24.68 25.94 25.17 24.21 0.00 0.00 -FBC 88 24.77 25.11 25.88 24.24 0.00 0.00 -FBC 89 24.09 25.62 25.34 24.95 0.00 0.00 -FBC 90 24.35 25.57 24.76 25.32 0.00 0.00 -FBC 91 25.17 25.07 25.31 24.45 0.00 0.00 -FBC 92 25.65 25.04 25.00 24.31 0.00 0.00 -FBC 93 25.04 25.51 25.04 24.41 0.00 0.00 -FBC 94 24.85 26.17 25.11 23.87 0.00 0.00 -FBC 95 24.81 25.37 25.50 24.32 0.00 0.00 -FBC 96 24.84 25.25 25.47 24.44 0.00 0.00 -FBC 97 24.61 25.47 25.27 24.65 0.00 0.00 -FBC 98 24.86 25.00 25.48 24.66 0.00 0.00 -FBC 99 23.74 25.30 25.96 25.00 0.00 0.00 -FBC 100 23.83 26.06 25.13 24.98 0.00 0.00 -# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters -FTC 246020 254592 253576 245812 0 -# ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] -LBC 1 24.05 25.38 26.27 24.30 0.00 0.00 -LBC 2 23.62 25.98 25.49 24.91 0.00 0.00 -LBC 3 23.93 25.62 26.32 24.13 0.00 0.00 -LBC 4 24.94 25.34 25.24 24.48 0.00 0.00 -LBC 5 24.69 25.34 25.35 24.62 0.00 0.00 -LBC 6 24.69 24.97 25.08 25.26 0.00 0.00 -LBC 7 24.10 25.17 26.68 24.05 0.00 0.00 -LBC 8 24.92 25.49 24.96 24.63 0.00 0.00 -LBC 9 24.23 25.94 24.81 25.02 0.00 0.00 -LBC 10 24.38 25.12 25.59 24.91 0.00 0.00 -LBC 11 24.42 25.60 25.75 24.23 0.00 0.00 -LBC 12 25.33 25.73 24.96 23.98 0.00 0.00 -LBC 13 25.35 24.51 26.17 23.97 0.00 0.00 -LBC 14 24.12 25.34 26.17 24.37 0.00 0.00 -LBC 15 24.77 25.23 25.13 24.87 0.00 0.00 -LBC 16 25.36 25.27 25.10 24.27 0.00 0.00 -LBC 17 24.88 24.93 25.68 24.51 0.00 0.00 -LBC 18 23.79 25.75 25.19 25.27 0.00 0.00 -LBC 19 24.43 25.82 24.93 24.82 0.00 0.00 -LBC 20 24.40 25.93 24.62 25.05 0.00 0.00 -LBC 21 25.88 24.75 25.12 24.25 0.00 0.00 -LBC 22 24.27 25.80 24.92 25.01 0.00 0.00 -LBC 23 24.61 25.95 25.28 24.16 0.00 0.00 -LBC 24 24.66 25.46 25.69 24.19 0.00 0.00 -LBC 25 24.09 25.61 25.73 24.57 0.00 0.00 -LBC 26 25.11 24.62 25.34 24.93 0.00 0.00 -LBC 27 24.51 26.23 24.74 24.52 0.00 0.00 -LBC 28 25.39 25.58 24.73 24.30 0.00 0.00 -LBC 29 24.85 25.62 24.90 24.63 0.00 0.00 -LBC 30 24.43 25.89 25.15 24.53 0.00 0.00 -LBC 31 24.70 25.53 25.58 24.19 0.00 0.00 -LBC 32 24.50 26.20 25.01 24.29 0.00 0.00 -LBC 33 23.88 25.74 25.43 24.95 0.00 0.00 -LBC 34 24.90 25.20 25.18 24.72 0.00 0.00 -LBC 35 24.16 25.63 25.75 24.46 0.00 0.00 -LBC 36 23.80 25.87 25.42 24.91 0.00 0.00 -LBC 37 24.96 25.03 26.27 23.74 0.00 0.00 -LBC 38 24.53 25.69 24.99 24.79 0.00 0.00 -LBC 39 23.96 25.89 24.70 25.45 0.00 0.00 -LBC 40 24.13 24.91 25.68 25.28 0.00 0.00 -LBC 41 24.32 25.44 25.03 25.21 0.00 0.00 -LBC 42 24.23 25.86 24.69 25.22 0.00 0.00 -LBC 43 24.44 25.74 24.60 25.22 0.00 0.00 -LBC 44 25.39 24.13 25.44 25.04 0.00 0.00 -LBC 45 24.68 25.90 25.28 24.14 0.00 0.00 -LBC 46 23.85 25.25 25.61 25.29 0.00 0.00 -LBC 47 25.20 23.57 26.09 25.14 0.00 0.00 -LBC 48 25.49 25.20 25.07 24.24 0.00 0.00 -LBC 49 25.12 25.47 25.15 24.26 0.00 0.00 -LBC 50 24.73 25.26 25.44 24.57 0.00 0.00 -LBC 51 25.43 25.54 24.96 24.07 0.00 0.00 -LBC 52 25.03 25.60 24.97 24.40 0.00 0.00 -LBC 53 25.63 25.45 24.67 24.25 0.00 0.00 -LBC 54 24.32 25.73 25.33 24.62 0.00 0.00 -LBC 55 23.73 25.22 25.57 25.48 0.00 0.00 -LBC 56 23.82 25.86 26.08 24.24 0.00 0.00 -LBC 57 24.82 24.65 25.22 25.31 0.00 0.00 -LBC 58 24.96 25.77 24.82 24.45 0.00 0.00 -LBC 59 24.16 26.01 25.42 24.41 0.00 0.00 -LBC 60 24.57 25.49 25.27 24.67 0.00 0.00 -LBC 61 24.56 25.46 25.66 24.32 0.00 0.00 -LBC 62 24.85 24.93 25.01 25.21 0.00 0.00 -LBC 63 24.54 24.82 25.87 24.77 0.00 0.00 -LBC 64 24.88 25.37 25.67 24.08 0.00 0.00 -LBC 65 24.49 25.02 26.39 24.10 0.00 0.00 -LBC 66 24.03 25.21 25.87 24.89 0.00 0.00 -LBC 67 24.37 24.94 25.79 24.90 0.00 0.00 -LBC 68 24.04 25.06 25.86 25.04 0.00 0.00 -LBC 69 24.44 25.11 25.49 24.95 0.01 0.00 -LBC 70 24.47 25.75 25.40 24.38 0.00 0.00 -LBC 71 24.31 25.94 25.55 24.20 0.00 0.00 -LBC 72 25.19 25.19 25.29 24.33 0.00 0.00 -LBC 73 24.78 25.82 25.31 24.09 0.00 0.00 -LBC 74 24.65 25.80 25.01 24.54 0.00 0.00 -LBC 75 24.70 25.09 25.57 24.64 0.00 0.00 -LBC 76 24.75 25.00 24.93 25.32 0.00 0.00 -LBC 77 24.61 25.39 25.07 24.93 0.00 0.00 -LBC 78 24.64 25.38 25.92 24.06 0.00 0.00 -LBC 79 25.21 25.97 24.86 23.96 0.00 0.00 -LBC 80 23.95 26.44 25.54 24.07 0.00 0.00 -LBC 81 25.06 25.25 26.07 23.62 0.00 0.00 -LBC 82 23.91 26.04 25.25 24.80 0.00 0.00 -LBC 83 25.01 25.52 25.44 24.03 0.00 0.00 -LBC 84 25.19 25.68 24.67 24.46 0.00 0.00 -LBC 85 24.81 25.27 24.82 25.10 0.00 0.00 -LBC 86 24.31 25.78 24.90 25.01 0.00 0.00 -LBC 87 24.94 24.98 25.55 24.53 0.00 0.00 -LBC 88 25.25 25.77 25.32 23.66 0.00 0.00 -LBC 89 25.07 25.91 24.94 24.08 0.00 0.00 -LBC 90 24.64 25.42 26.18 23.76 0.00 0.00 -LBC 91 24.92 25.38 25.24 24.46 0.00 0.00 -LBC 92 24.47 25.18 25.08 25.27 0.00 0.00 -LBC 93 25.02 25.58 24.58 24.82 0.00 0.00 -LBC 94 24.05 25.41 24.94 25.60 0.00 0.00 -LBC 95 24.91 25.05 25.08 24.96 0.00 0.00 -LBC 96 24.10 25.22 25.74 24.94 0.00 0.00 -LBC 97 24.56 24.56 25.68 25.20 0.00 0.00 -LBC 98 25.34 25.16 25.36 24.14 0.00 0.00 -LBC 99 24.80 25.47 25.70 24.03 0.00 0.00 -LBC 100 23.53 26.05 26.10 24.32 0.00 0.00 -# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters -LTC 246099 254317 253651 245932 1 -# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs -IS 0 0 0 0 0 -IS 1 0 0 0 0 -IS 2 0 0 0 0 -IS 3 0 0 0 0 -IS 4 0 0 0 0 -IS 5 0 0 0 0 -IS 6 0 0 0 0 -IS 7 0 0 0 0 -IS 8 0 0 0 0 -IS 9 0 0 0 0 -IS 10 0 0 0 0 -IS 11 0 0 0 0 -IS 12 0 0 0 0 -IS 13 0 0 0 0 -IS 14 0 0 0 0 -IS 15 0 0 0 0 -IS 16 0 0 0 0 -IS 17 0 0 0 0 -IS 18 0 0 0 0 -IS 19 0 0 0 0 -IS 20 0 0 0 0 -IS 21 0 0 0 0 -IS 22 0 0 0 0 -IS 23 0 0 0 0 -IS 24 0 0 0 0 -IS 25 0 0 0 0 -IS 26 0 0 0 0 -IS 27 0 0 0 0 -IS 28 0 0 0 0 -IS 29 0 0 0 0 -IS 30 0 0 0 0 -IS 31 0 0 0 0 -IS 32 0 0 0 0 -IS 33 0 0 0 0 -IS 34 0 0 0 0 -IS 35 0 0 0 0 -IS 36 0 0 0 0 -IS 37 0 0 0 0 -IS 38 0 0 0 0 -IS 39 0 0 0 0 -IS 40 0 0 0 0 -IS 41 0 0 0 0 -IS 42 0 0 0 0 -IS 43 0 0 0 0 -IS 44 0 0 0 0 -IS 45 0 0 0 0 -IS 46 0 0 0 0 -IS 47 0 0 0 0 -IS 48 0 0 0 0 -IS 49 0 0 0 0 -IS 50 0 0 0 0 -IS 51 0 0 0 0 -IS 52 0 0 0 0 -IS 53 0 0 0 0 -IS 54 0 0 0 0 -IS 55 0 0 0 0 -IS 56 0 0 0 0 -IS 57 0 0 0 0 -IS 58 0 0 0 0 -IS 59 0 0 0 0 -IS 60 0 0 0 0 -IS 61 0 0 0 0 -IS 62 0 0 0 0 -IS 63 0 0 0 0 -IS 64 0 0 0 0 -IS 65 0 0 0 0 -IS 66 0 0 0 0 -IS 67 0 0 0 0 -IS 68 0 0 0 0 -IS 69 36 0 36 0 -IS 70 11 0 11 0 -IS 71 30 0 30 0 -IS 72 24 0 24 0 -IS 73 34 0 34 0 -IS 74 25 0 25 0 -IS 75 30 0 30 0 -IS 76 22 0 22 0 -IS 77 26 0 26 0 -IS 78 24 0 24 0 -IS 79 30 0 30 0 -IS 80 25 0 25 0 -IS 81 33 0 33 0 -IS 82 33 0 33 0 -IS 83 27 0 27 0 -IS 84 26 0 26 0 -IS 85 36 0 36 0 -IS 86 26 0 26 0 -IS 87 26 0 26 0 -IS 88 34 0 34 0 -IS 89 24 0 24 0 -IS 90 33 0 33 0 -IS 91 35 0 35 0 -IS 92 40 0 40 0 -IS 93 37 0 37 0 -IS 94 20 0 20 0 -IS 95 30 0 30 0 -IS 96 26 0 26 0 -IS 97 33 0 33 0 -IS 98 29 0 29 0 -IS 99 30 0 30 0 -IS 100 33 15 18 0 -IS 101 27 27 0 0 -IS 102 29 29 0 0 -IS 103 37 37 0 0 -IS 104 32 32 0 0 -IS 105 26 26 0 0 -IS 106 38 38 0 0 -IS 107 26 26 0 0 -IS 108 32 32 0 0 -IS 109 26 26 0 0 -IS 110 29 29 0 0 -IS 111 43 43 0 0 -IS 112 26 26 0 0 -IS 113 20 20 0 0 -IS 114 34 34 0 0 -IS 115 32 32 0 0 -IS 116 32 32 0 0 -IS 117 52 52 0 0 -IS 118 30 30 0 0 -IS 119 29 29 0 0 -IS 120 28 28 0 0 -IS 121 35 35 0 0 -IS 122 25 25 0 0 -IS 123 34 34 0 0 -IS 124 22 22 0 0 -IS 125 20 20 0 0 -IS 126 38 38 0 0 -IS 127 30 30 0 0 -IS 128 32 32 0 0 -IS 129 31 31 0 0 -IS 130 33 33 0 0 -IS 131 32 32 0 0 -IS 132 22 22 0 0 -IS 133 35 35 0 0 -IS 134 30 30 0 0 -IS 135 28 28 0 0 -IS 136 33 33 0 0 -IS 137 28 28 0 0 -IS 138 29 29 0 0 -IS 139 31 31 0 0 -IS 140 34 34 0 0 -IS 141 37 37 0 0 -IS 142 30 30 0 0 -IS 143 30 30 0 0 -IS 144 27 27 0 0 -IS 145 24 24 0 0 -IS 146 26 26 0 0 -IS 147 33 33 0 0 -IS 148 33 33 0 0 -IS 149 28 28 0 0 -IS 150 25 25 0 0 -IS 151 25 25 0 0 -IS 152 24 24 0 0 -IS 153 24 24 0 0 -IS 154 33 33 0 0 -IS 155 36 36 0 0 -IS 156 21 21 0 0 -IS 157 26 26 0 0 -IS 158 26 26 0 0 -IS 159 27 27 0 0 -IS 160 27 27 0 0 -IS 161 34 34 0 0 -IS 162 28 28 0 0 -IS 163 27 27 0 0 -IS 164 28 28 0 0 -IS 165 25 25 0 0 -IS 166 34 34 0 0 -IS 167 24 24 0 0 -IS 168 41 41 0 0 -IS 169 26 26 0 0 -IS 170 34 34 0 0 -IS 171 28 28 0 0 -IS 172 30 30 0 0 -IS 173 28 28 0 0 -IS 174 26 26 0 0 -IS 175 29 29 0 0 -IS 176 37 37 0 0 -IS 177 35 35 0 0 -IS 178 28 28 0 0 -IS 179 25 25 0 0 -IS 180 25 25 0 0 -IS 181 36 36 0 0 -IS 182 31 31 0 0 -IS 183 25 25 0 0 -IS 184 29 29 0 0 -IS 185 32 32 0 0 -IS 186 24 24 0 0 -IS 187 27 27 0 0 -IS 188 31 31 0 0 -IS 189 34 34 0 0 -IS 190 45 45 0 0 -IS 191 32 32 0 0 -IS 192 20 20 0 0 -IS 193 41 41 0 0 -IS 194 30 30 0 0 -IS 195 31 31 0 0 -IS 196 24 24 0 0 -IS 197 36 36 0 0 -IS 198 27 27 0 0 -IS 199 30 30 0 0 -IS 200 30 30 0 0 -IS 201 26 26 0 0 -IS 202 40 40 0 0 -IS 203 37 37 0 0 -IS 204 37 37 0 0 -IS 205 28 28 0 0 -IS 206 33 33 0 0 -IS 207 28 28 0 0 -IS 208 31 31 0 0 -IS 209 37 37 0 0 -IS 210 28 28 0 0 -IS 211 31 31 0 0 -IS 212 32 32 0 0 -IS 213 33 33 0 0 -IS 214 33 33 0 0 -IS 215 29 29 0 0 -IS 216 28 28 0 0 -IS 217 33 33 0 0 -IS 218 27 27 0 0 -IS 219 22 22 0 0 -IS 220 31 31 0 0 -IS 221 38 38 0 0 -IS 222 29 29 0 0 -IS 223 41 41 0 0 -IS 224 22 22 0 0 -IS 225 28 28 0 0 -IS 226 29 29 0 0 -IS 227 26 26 0 0 -IS 228 26 26 0 0 -IS 229 33 33 0 0 -IS 230 21 21 0 0 -IS 231 24 24 0 0 -IS 232 31 31 0 0 -IS 233 33 33 0 0 -IS 234 23 23 0 0 -IS 235 29 29 0 0 -IS 236 30 30 0 0 -IS 237 31 31 0 0 -IS 238 33 33 0 0 -IS 239 31 31 0 0 -IS 240 25 25 0 0 -IS 241 29 29 0 0 -IS 242 40 40 0 0 -IS 243 24 24 0 0 -IS 244 29 29 0 0 -IS 245 39 39 0 0 -IS 246 32 32 0 0 -IS 247 40 40 0 0 -IS 248 30 30 0 0 -IS 249 29 29 0 0 -IS 250 32 32 0 0 -IS 251 22 22 0 0 -IS 252 33 33 0 0 -IS 253 33 33 0 0 -IS 254 27 27 0 0 -IS 255 28 28 0 0 -IS 256 19 19 0 0 -IS 257 39 39 0 0 -IS 258 27 27 0 0 -IS 259 34 34 0 0 -IS 260 30 30 0 0 -IS 261 36 36 0 0 -IS 262 34 34 0 0 -IS 263 32 32 0 0 -IS 264 34 34 0 0 -IS 265 19 19 0 0 -IS 266 45 45 0 0 -IS 267 29 29 0 0 -IS 268 38 38 0 0 -IS 269 28 28 0 0 -IS 270 27 27 0 0 -IS 271 26 26 0 0 -IS 272 35 35 0 0 -IS 273 31 31 0 0 -IS 274 31 31 0 0 -IS 275 25 25 0 0 -IS 276 23 23 0 0 -IS 277 35 35 0 0 -IS 278 31 31 0 0 -IS 279 35 35 0 0 -IS 280 27 27 0 0 -IS 281 35 35 0 0 -IS 282 28 28 0 0 -IS 283 30 30 0 0 -IS 284 19 19 0 0 -IS 285 30 30 0 0 -IS 286 31 31 0 0 -IS 287 28 28 0 0 -IS 288 28 28 0 0 -IS 289 42 42 0 0 -IS 290 34 34 0 0 -IS 291 32 32 0 0 -IS 292 36 36 0 0 -IS 293 33 33 0 0 -IS 294 34 34 0 0 -IS 295 29 29 0 0 -IS 296 26 26 0 0 -IS 297 19 19 0 0 -IS 298 37 37 0 0 -IS 299 24 24 0 0 -IS 300 29 29 0 0 -IS 301 25 25 0 0 -IS 302 26 26 0 0 -IS 303 43 43 0 0 -IS 304 31 31 0 0 -IS 305 30 30 0 0 -IS 306 28 28 0 0 -IS 307 29 29 0 0 -IS 308 35 35 0 0 -IS 309 35 35 0 0 -IS 310 29 29 0 0 -IS 311 35 35 0 0 -IS 312 30 30 0 0 -IS 313 48 48 0 0 -IS 314 17 17 0 0 -IS 315 26 26 0 0 -IS 316 25 25 0 0 -IS 317 28 28 0 0 -IS 318 31 31 0 0 -IS 319 33 33 0 0 -IS 320 36 36 0 0 -IS 321 30 30 0 0 -IS 322 34 34 0 0 -IS 323 30 30 0 0 -IS 324 38 38 0 0 -IS 325 34 34 0 0 -IS 326 23 23 0 0 -IS 327 28 28 0 0 -IS 328 37 37 0 0 -IS 329 26 26 0 0 -IS 330 30 30 0 0 -IS 331 37 37 0 0 -IS 332 33 33 0 0 -IS 333 28 28 0 0 -IS 334 28 28 0 0 -IS 335 37 37 0 0 -IS 336 42 42 0 0 -IS 337 30 30 0 0 -IS 338 33 33 0 0 -IS 339 32 32 0 0 -IS 340 37 37 0 0 -IS 341 26 26 0 0 -IS 342 37 37 0 0 -IS 343 29 29 0 0 -IS 344 23 23 0 0 -IS 345 35 35 0 0 -IS 346 25 25 0 0 -IS 347 33 33 0 0 -IS 348 34 34 0 0 -IS 349 37 37 0 0 -IS 350 30 30 0 0 -IS 351 23 23 0 0 -IS 352 30 30 0 0 -IS 353 30 30 0 0 -IS 354 35 35 0 0 -IS 355 30 30 0 0 -IS 356 28 28 0 0 -IS 357 26 26 0 0 -IS 358 31 31 0 0 -IS 359 28 28 0 0 -IS 360 27 27 0 0 -IS 361 32 32 0 0 -IS 362 30 30 0 0 -IS 363 26 26 0 0 -IS 364 29 29 0 0 -IS 365 40 40 0 0 -IS 366 33 33 0 0 -IS 367 38 38 0 0 -IS 368 27 27 0 0 -IS 369 34 34 0 0 -IS 370 43 43 0 0 -IS 371 27 27 0 0 -IS 372 35 35 0 0 -IS 373 27 27 0 0 -IS 374 24 24 0 0 -IS 375 30 30 0 0 -IS 376 36 36 0 0 -IS 377 24 24 0 0 -IS 378 30 30 0 0 -IS 379 35 35 0 0 -IS 380 26 26 0 0 -IS 381 32 32 0 0 -IS 382 34 34 0 0 -IS 383 34 34 0 0 -IS 384 34 34 0 0 -IS 385 21 21 0 0 -IS 386 34 34 0 0 -IS 387 35 35 0 0 -IS 388 29 29 0 0 -IS 389 25 25 0 0 -IS 390 24 24 0 0 -IS 391 25 25 0 0 -IS 392 29 29 0 0 -IS 393 32 32 0 0 -IS 394 33 33 0 0 -IS 395 27 27 0 0 -# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count -RL 100 20000 -# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count -FRL 100 10000 -# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count -LRL 100 10000 -# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions -# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) -# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. -COV [1-1] 1 1059236 -COV [2-2] 2 327748 -COV [3-3] 3 71636 -COV [4-4] 4 14151 -COV [5-5] 5 2032 -COV [6-6] 6 562 -COV [7-7] 7 32 -# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile -GCD 0.0 0.862 0.000 0.000 0.000 0.000 0.000 -GCD 1.6 1.293 0.020 0.020 0.020 0.020 0.020 -GCD 39.0 1.724 0.440 0.440 0.440 0.440 0.440 -GCD 41.0 2.155 0.290 0.290 0.290 0.290 0.290 -GCD 43.0 2.586 0.385 0.385 0.385 0.385 0.385 -GCD 44.0 3.448 0.415 0.415 0.425 0.435 0.435 -GCD 45.0 4.310 0.345 0.345 0.428 0.510 0.510 -GCD 46.0 5.603 0.395 0.395 0.405 0.535 0.535 -GCD 47.0 9.052 0.345 0.376 0.447 0.533 0.605 -GCD 48.0 15.948 0.344 0.387 0.442 0.490 0.512 -GCD 49.0 23.707 0.367 0.399 0.430 0.481 0.563 -GCD 50.0 38.362 0.357 0.374 0.407 0.440 0.480 -GCD 51.0 58.190 0.325 0.375 0.423 0.482 0.520 -GCD 52.0 78.879 0.380 0.415 0.440 0.474 0.525 -GCD 53.0 93.103 0.364 0.410 0.450 0.477 0.516 -GCD 54.0 98.707 0.346 0.395 0.430 0.450 0.549 -GCD 55.0 99.138 0.450 0.450 0.450 0.450 0.450 -GCD 56.0 100.000 0.410 0.410 0.412 0.415 0.415 diff --git a/tests/software/samtools/main.nf b/tests/software/samtools/main.nf index b11f655f..747a1293 100644 --- a/tests/software/samtools/main.nf +++ b/tests/software/samtools/main.nf @@ -6,6 +6,7 @@ include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] ) include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addParams( options: [:] ) include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] ) +include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] ) workflow test_samtools_flagstat { @@ -45,3 +46,13 @@ workflow test_samtools_sort { SAMTOOLS_SORT ( input ) } + +workflow test_samtools_stats { + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true), + file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ] + + SAMTOOLS_STATS ( input ) +} diff --git a/tests/software/samtools/test.yml b/tests/software/samtools/test.yml index 55ff561c..d4e61907 100644 --- a/tests/software/samtools/test.yml +++ b/tests/software/samtools/test.yml @@ -33,3 +33,12 @@ files: - path: output/samtools/test.bam md5sum: a41bfadacd2eeef1d31e05c135cc4f4e + +- name: Run samtools stats test workflow + command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_stats -c tests/config/nextflow.config + tags: + - samtools + - samtools_stats + files: + - path: output/samtools/test.paired_end.sorted.bam.stats + md5sum: 06c183864d6e47ab89b0650cae831a93