Get samtools flagstat passing

software/samtools/flagstat/meta.yml

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+name: samtools_flagstat
+description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type
+keywords:
+    - stats
+    - mapping
+    - counts
+    - bam
+    - sam
+    - cram
+tools:
+    - samtools:
+        description: |
+            SAMtools is a set of utilities for interacting with and post-processing
+            short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+            These files are generated as output by short read aligners like BWA.
+        homepage: http://www.htslib.org/
+        documentation: hhttp://www.htslib.org/doc/samtools.html
+        doi: 10.1093/bioinformatics/btp352
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+    - bai:
+        type: file
+        description: Index for BAM/CRAM/SAM file
+        pattern: "*.{bai,crai,sai}"
+    - options:
+        type: map
+        description: |
+            Groovy Map containing module options for passing command-line arguments and
+            output file paths.
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - flagstat:
+        type: file
+        description: File containing samtools flagstat output
+        pattern: "*.{flagstat}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@drpatelh"

software/samtools/flagstat/test/output/samtools/test.paired_end.sorted.bam.flagstat

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+20000 + 0 in total (QC-passed reads + QC-failed reads)
+0 + 0 secondary
+0 + 0 supplementary
+0 + 0 duplicates
+20000 + 0 mapped (100.00% : N/A)
+20000 + 0 paired in sequencing
+10000 + 0 read1
+10000 + 0 read2
+20000 + 0 properly paired (100.00% : N/A)
+20000 + 0 with itself and mate mapped
+0 + 0 singletons (0.00% : N/A)
+0 + 0 with mate mapped to a different chr
+0 + 0 with mate mapped to a different chr (mapQ>=5)