Multithreaded samtools commands (#2080)

* Multithreaded samtools commands

* Updated the checksums since the BAM files include the actual command line

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

modules/samtools/ampliconclip/main.nf

@@ -31,6 +31,7 @@ process SAMTOOLS_AMPLICONCLIP {
     """
     samtools \\
         ampliconclip \\
+        --threads ${task.cpus-1} \\
         $args \\
         $rejects \\
         $stats \\

modules/samtools/depth/main.nf

@@ -23,6 +23,7 @@ process SAMTOOLS_DEPTH {
     """
     samtools \\
         depth \\
+        --threads ${task.cpus-1} \\
         $args \\
         -o ${prefix}.tsv \\
         $bam

modules/samtools/idxstats/main.nf

@@ -24,6 +24,7 @@ process SAMTOOLS_IDXSTATS {
     """
     samtools \\
         idxstats \\
+        --threads ${task.cpus-1} \\
         $bam \\
         > ${prefix}.idxstats
 

tests/modules/samtools/ampliconclip/test.yml

@@ -5,7 +5,7 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: d270363a7fb3d96be2df211099efc75b
+      md5sum: 69e4ba713447864231f6cbbaf036c51d
 
 - name: samtools ampliconclip no stats with rejects
   command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
@@ -14,9 +14,9 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: e7c4e64c259212e1670f6de96a5549b4
+      md5sum: dd2ed9d7cc4ddc070ece2dccc577f94b
     - path: output/samtools/test.cliprejects.bam
-      md5sum: b7c057b11950c2271a0c92236bee94b7
+      md5sum: 7d641f6da838f41d75eaabbd897f60bd
 
 - name: samtools ampliconclip with stats with rejects
   command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
@@ -25,8 +25,8 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: e75992d4ff69cbaed9a089231be86b5e
+      md5sum: 6c19afc0873fba2f4e530eabf61c0735
     - path: output/samtools/test.cliprejects.bam
-      md5sum: 729f03e7a2801d2c56c32bef8f3d6ead
+      md5sum: 1dfb61aa80d8e90add324ed61ed17061
     - path: output/samtools/test.clipstats.txt
-      md5sum: fc23355e1743d47f2541f2cb1a7a0cda
+      md5sum: 05ead360a98fab6a678056e326c4f1f3