feat: added samtools wrapper utils (#454)

* Added wrapper_utils, some tempdirs, extra doc, and code clean-up

* Added IDX generation to test

* Fixed missing import and log file

* Added more log files to tests

* Fixed log redirection

* Added author

bio/samtools/calmd/environment.yaml

@@ -2,4 +2,5 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - samtools ==1.11
+  - samtools =1.14
+  - snakemake-wrapper-utils =0.3

bio/samtools/calmd/meta.yaml

@@ -1,4 +1,7 @@
 name: samtools calmd
-description: Calculates MD and NM tags. For more information see `SAMtools documentation <http://www.htslib.org/doc/samtools-calmd.html>`_.
+description: Calculates MD and NM tags.
 authors:
   - Filipe G. Vieira
+notes: |
+  * The `extra` param allows for additional program arguments (not `-@/--threads` or `-O/--output-fmt`).
+  * For more information see, http://www.htslib.org/doc/samtools-calmd.html

bio/samtools/calmd/test/Snakefile

@@ -1,11 +1,13 @@
 rule samtools_calmd:
     input:
-        aln = "{sample}.bam", # Can be 'sam', 'bam', or 'cram'
-        ref = "genome.fasta"
+        aln="{sample}.bam",  # Can be 'sam', 'bam', or 'cram'
+        ref="genome.fasta",
     output:
-        "{sample}.calmd.bam"
+        "{sample}.calmd.bam",
+    log:
+        "{sample}.calmd.log",
     params:
-        "-E" # optional params string
+        extra="-E",  # optional params string
     threads: 2
     wrapper:
         "master/bio/samtools/calmd"

bio/samtools/calmd/wrapper.py

@@ -3,14 +3,15 @@
 __license__ = "MIT"
 
 
-from os import path
 from snakemake.shell import shell
+from snakemake_wrapper_utils.samtools import get_samtools_opts
 
+samtools_opts = get_samtools_opts(
+    snakemake, parse_write_index=False, parse_output=False
+)
+extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 
-out_name, out_ext = path.splitext(snakemake.output[0])
-out_ext = out_ext[1:].upper()
-
 shell(
-    "samtools calmd --threads {snakemake.threads} {snakemake.params} --output-fmt {out_ext} {snakemake.input.aln} {snakemake.input.ref} > {snakemake.output[0]} {log}"
+    "samtools calmd {samtools_opts} {extra} {snakemake.input.aln} {snakemake.input.ref} > {snakemake.output[0]} {log}"
 )

bio/samtools/depth/environment.yaml

@@ -2,4 +2,5 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - samtools ==1.10
+  - samtools =1.14
+  - snakemake-wrapper-utils =0.3

bio/samtools/depth/meta.yaml

@@ -1,4 +1,8 @@
 name: samtools depth
-description: Compute the read depth at each position or region using samtools. For more information see `SAMtools documentation <http://www.htslib.org/doc/samtools-depth.html>`_.
+description: Compute the read depth at each position or region using samtools.
 authors:
   - Dayne Filer
+  - Filipe G. Vieira
+notes: |
+  * The `extra` param allows for additional program arguments (not `-@/--threads` or `-o`).
+  * For more information see, http://www.htslib.org/doc/samtools-depth.html

bio/samtools/depth/test/Snakefile

@@ -1,11 +1,13 @@
 rule samtools_depth:
     input:
         bams=["mapped/A.bam", "mapped/B.bam"],
-        bed="regionToCalcDepth.bed", # optional
+        bed="regionToCalcDepth.bed",  # optional
     output:
-        "depth.txt"
+        "depth.txt",
+    log:
+        "depth.log",
     params:
         # optional bed file passed to -b
-        extra="" # optional additional parameters as string
+        extra="",  # optional additional parameters as string
     wrapper:
         "master/bio/samtools/depth"

bio/samtools/depth/wrapper.py

@@ -6,17 +6,17 @@
 __license__ = "MIT"
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.samtools import get_samtools_opts
 
+samtools_opts = get_samtools_opts(
+    snakemake, parse_write_index=False, parse_output_format=False
+)
+extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
-params = snakemake.params.get("extra", "")
-
 # check for optional bed file
 bed = snakemake.input.get("bed", "")
 if bed:
     bed = "-b " + bed
 
-shell(
-    "samtools depth {params} {bed} "
-    "-o {snakemake.output[0]} {snakemake.input.bams} {log}"
-)
+shell("samtools depth {samtools_opts} {extra} {bed} {snakemake.input.bams} {log}")

bio/samtools/faidx/environment.yaml

@@ -2,4 +2,5 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - samtools ==1.10
+  - samtools =1.14
+  - snakemake-wrapper-utils =0.3

bio/samtools/faidx/meta.yaml

@@ -1,8 +1,12 @@
 name: samtools faidx
-description: index reference sequence in FASTA format from reference sequence. For more information see `SAMtools documentation <http://www.htslib.org/doc/samtools-faidx.html>`_.
+description: index reference sequence in FASTA format from reference sequence.
 authors:
   - Michael Chambers
+  - Filipe G. Vieira
 input:
   - reference sequence file (.fa)
 output:
   - indexed reference sequence file (.fai)
+notes: |
+  * The `extra` param allows for additional program arguments (not `-o`).
+  * For more information see, http://www.htslib.org/doc/samtools-faidx.html

bio/samtools/faidx/test/Snakefile

@@ -1,9 +1,11 @@
 rule samtools_index:
     input:
-        "{sample}.fa"
+        "{sample}.fa",
     output:
-        "{sample}.fa.fai"
+        "{sample}.fa.fai",
+    log:
+        "{sample}.log",
     params:
-        "" # optional params string
+        extra="",  # optional params string
     wrapper:
         "master/bio/samtools/faidx"

bio/samtools/faidx/wrapper.py

@@ -5,9 +5,12 @@
 
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.samtools import get_samtools_opts
 
-log = snakemake.log_fmt_shell(stdout=False, stderr=True)
-
-shell(
-    "samtools faidx {snakemake.params} {snakemake.input[0]} > {snakemake.output[0]} {log}"
+samtools_opts = get_samtools_opts(
+    snakemake, parse_threads=False, parse_write_index=False, parse_output_format=False
 )
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+shell("samtools faidx {samtools_opts} {extra} {snakemake.input[0]} {log}")

bio/samtools/fastq/interleaved/environment.yaml

@@ -3,3 +3,4 @@ channels:
   - bioconda
 dependencies:
   - samtools =1.14
+  - snakemake-wrapper-utils =0.3

bio/samtools/fastq/interleaved/meta.yaml

@@ -7,4 +7,5 @@ authors:
   - Victoria Sack
   - Filipe G. Vieira
 notes: |
+  * The `extra` param allows for additional program arguments (not `-@/--threads` or `-o`).
   * For more information see, http://www.htslib.org/doc/samtools-fasta.html

bio/samtools/fastq/interleaved/wrapper.py

@@ -6,15 +6,12 @@
 
 import os
 from snakemake.shell import shell
+from snakemake_wrapper_utils.samtools import get_samtools_opts
 
+samtools_opts = get_samtools_opts(
+    snakemake, parse_write_index=False, parse_output_format=False
+)
+extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 
-prefix = os.path.splitext(snakemake.output[0])[0]
-
-shell(
-    "samtools fastq {snakemake.params} "
-    " -@ {snakemake.threads} "
-    " {snakemake.input[0]}"
-    " > {snakemake.output[0]} "
-    "{log}"
-)
+shell("samtools fastq {samtools_opts} {extra} {snakemake.input[0]} {log}")

bio/samtools/fastq/separate/meta.yaml

@@ -9,5 +9,5 @@ authors:
   - Victoria Sack
   - Filipe G. Vieira
 notes: |
-  * Samtools -@/--threads takes one integer as input. This is the number of additional threads and not raw threads.
+  * The `extra` param allows for additional program arguments.
   * For more information see, http://www.htslib.org/doc/samtools-fasta.html

bio/samtools/fastx/environment.yaml

@@ -4,4 +4,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - samtools==1.12
+  - samtools =1.14
+  - snakemake-wrapper-utils =0.3

bio/samtools/fastx/meta.yaml

@@ -2,7 +2,11 @@ name: samtools fastx
 description: Converts a SAM, BAM or CRAM into FASTQ or FASTA format.
 authors:
   - William Rowell
+  - Filipe G. Vieira
 input:
   - bam or sam file (.bam, .sam)
 output:
   - fastq file (.fastq) or fasta file (.fasta)
+notes: |
+  * The `extra` param allows for additional program arguments (not `-@/--threads` or `-o`).
+  * For more information see, http://www.htslib.org/doc/samtools-fasta.html

bio/samtools/fastx/test/Snakefile

@@ -7,10 +7,10 @@ rule samtools_fastq:
         "{prefix}.log",
     message:
         ""
-    threads:  # Samtools takes additional threads through its option -@
-        2     # This value - 1 will be sent to -@
+    # Samtools takes additional threads through its option -@
+    threads: 2  # This value - 1 will be sent to -@
     params:
-        outputtype = "fasta",
-        extra = ""
+        outputtype="fasta",
+        extra="",
     wrapper:
         "master/bio/samtools/fastx/"

bio/samtools/fastx/wrapper.py

@@ -5,19 +5,15 @@
 
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.samtools import get_samtools_opts
 
-log = snakemake.log_fmt_shell(stdout=False, stderr=True)
-
+samtools_opts = get_samtools_opts(
+    snakemake, parse_write_index=False, parse_output_format=False
+)
 extra = snakemake.params.get("extra", "")
-# Samtools takes additional threads through its option -@
-# One thread for samtools merge
-# Other threads are *additional* threads passed to the '-@' argument
-threads = "" if snakemake.threads <= 1 else " -@ {} ".format(snakemake.threads - 1)
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
 
 shell(
-    """
-    (samtools {snakemake.params.outputtype} \
-        {threads} {extra} \
-        {snakemake.input} > {snakemake.output}) {log}
-    """
+    "samtools {snakemake.params.outputtype} {samtools_opts} {extra} {snakemake.input} {log}"
 )

bio/samtools/fixmate/environment.yaml

@@ -4,4 +4,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - samtools ==1.10
+  - samtools =1.14
+  - snakemake-wrapper-utils =0.3

bio/samtools/fixmate/meta.yaml

@@ -1,8 +1,12 @@
 name: samtools fixmate
-description: Use samtools to correct mate information after BWA mapping. For more information see `SAMtools documentation <http://www.htslib.org/doc/samtools-fixmate.html>`_.
+description: Use samtools to correct mate information after BWA mapping.
 authors:
   - Thibault Dayris
+  - Filipe G. Vieira
 input:
   - bam or sam file (.bam,.sam)
 output:
   - bam or sam file (.bam,.sam)
+notes: |
+  * The `extra` param allows for additional program arguments (not `-@/--threads` or `-O/--output-fmt`).
+  * For more information see, http://www.htslib.org/doc/samtools-fixmate.html

bio/samtools/fixmate/test/Snakefile

@@ -1,13 +1,14 @@
 rule samtools_fixmate:
     input:
-        "mapped/{input}"
+        "mapped/{input}",
     output:
-        "fixed/{input}"
+        "fixed/{input}",
+    log:
+        "{input}.log",
     message:
         "Fixing mate information in {wildcards.input}"
-    threads:
-        1
+    threads: 1
     params:
-        extra = ""
+        extra="",
     wrapper:
         "master/bio/samtools/fixmate/"

bio/samtools/fixmate/wrapper.py

@@ -5,22 +5,16 @@
 __email__ = "thibault.dayris@gustaveroussy.fr"
 __license__ = "MIT"
 
-import os.path as op
-
 from snakemake.shell import shell
 from snakemake.utils import makedirs
+from snakemake_wrapper_utils.samtools import get_samtools_opts
 
-log = snakemake.log_fmt_shell(stdout=True, stderr=True)
-
+samtools_opts = get_samtools_opts(
+    snakemake, parse_write_index=False, parse_output=False
+)
 extra = snakemake.params.get("extra", "")
-
-# Samtools' threads parameter lists ADDITIONAL threads.
-# that is why threads - 1 has to be given to the -@ parameter
-threads = "" if snakemake.threads <= 1 else " -@ {} ".format(snakemake.threads - 1)
-
-makedirs(op.dirname(snakemake.output[0]))
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
 shell(
-    "samtools fixmate {extra} {threads}"
-    " {snakemake.input[0]} {snakemake.output[0]} {log}"
+    "samtools fixmate {samtools_opts} {extra} {snakemake.input[0]} {snakemake.output[0]} {log}"
 )

bio/samtools/flagstat/environment.yaml

@@ -2,4 +2,5 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - samtools ==1.10
+  - samtools =1.14
+  - snakemake-wrapper-utils =0.3

bio/samtools/flagstat/meta.yaml

@@ -1,8 +1,12 @@
 name: samtools flagstat
-description: Use samtools to create a flagstat file from a bam or sam file. For more information see `SAMtools documentation <http://www.htslib.org/doc/samtools-flagstat.html>`_.
+description: Use samtools to create a flagstat file from a bam or sam file.
 authors:
   - Christopher Preusch
+  - Filipe G. Vieira
 input:
   - bam or sam file (.bam,.sam)
 output:
   - flagstat file (.flagstat)
+notes: |
+  * The `extra` param allows for additional program arguments (not `-@/--threads`).
+  * For more information see, http://www.htslib.org/doc/samtools-flagstat.html

bio/samtools/flagstat/test/Snakefile

@@ -1,7 +1,11 @@
 rule samtools_flagstat:
     input:
-        "mapped/{sample}.bam"
+        "mapped/{sample}.bam",
     output:
-        "mapped/{sample}.bam.flagstat"
+        "mapped/{sample}.bam.flagstat",
+    log:
+        "{sample}.log",
+    params:
+        extra="",  # optional params string
     wrapper:
         "master/bio/samtools/flagstat"

bio/samtools/flagstat/wrapper.py

@@ -5,7 +5,14 @@
 
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.samtools import get_samtools_opts
 
+samtools_opts = get_samtools_opts(
+    snakemake, parse_write_index=False, parse_output=False, parse_output_format=False
+)
+extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 
-shell("samtools flagstat {snakemake.input[0]} > {snakemake.output[0]} {log}")
+shell(
+    "samtools flagstat {samtools_opts} {extra} {snakemake.input[0]} > {snakemake.output[0]} {log}"
+)

bio/samtools/idxstats/environment.yaml

@@ -2,4 +2,5 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - samtools ==1.10
+  - samtools =1.14
+  - snakemake-wrapper-utils =0.3