fix: fixed GATK3 conda channel priorities and code reformat (#534)

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### Description

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Fixed conda channel priorities, plus some code clean-up

### QC
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* [x] I confirm that:

For all wrappers added by this PR, 

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

bio/gatk/applybqsr/environment.yaml

@@ -3,7 +3,7 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - gatk4 =4.2
+  - gatk4 =4.3.0.0
   - openjdk =8
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5
   - samtools =1.16

bio/gatk/applyvqsr/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/baserecalibrator/environment.yaml

@@ -4,5 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - openjdk =8
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/baserecalibratorspark/environment.yaml

@@ -4,5 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - openjdk =8
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/cleansam/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/combinegvcfs/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/depthofcoverage/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.4
+  - snakemake-wrapper-utils =0.5

bio/gatk/estimatelibrarycomplexity/environment.yaml

@@ -3,5 +3,5 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - gatk4 =4.2
+  - snakemake-wrapper-utils =0.5

bio/gatk/filtermutectcalls/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/genomicsdbimport/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/genotypegvcfs/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/getpileupsummaries/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/learnreadorientationmodel/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/markduplicatesspark/environment.yaml

@@ -5,4 +5,4 @@ channels:
 dependencies:
   - gatk4 =4.2
   - openjdk =8
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/mutect/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/selectvariants/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/splitncigarreads/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/varianteval/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/variantfiltration/environment.yaml

@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5

bio/gatk/variantrecalibrator/environment.yaml

@@ -4,6 +4,6 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5
   - google-cloud-sdk
   - google-crc32c

bio/gatk3/baserecalibrator/environment.yaml

@@ -3,5 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - gatk ==3.8
-  - snakemake-wrapper-utils ==0.1.3
+  - gatk =3.8
+  - python >=3.10
+  - snakemake-wrapper-utils =0.5

bio/gatk3/baserecalibrator/test/Snakefile

@@ -1,16 +1,20 @@
 rule baserecalibrator:
     input:
-        bam="mapped/{sample}.bam",
+        bam="{sample}.bam",
+        bai="{sample}.bai",
         ref="genome.fasta",
-        known="dbsnp.vcf.gz"
+        fai="genome.fasta.fai",
+        dict="genome.dict",
+        known="dbsnp.vcf.gz",
+        known_idx="dbsnp.vcf.gz.tbi",
     output:
-        "{sample}.recal_data_table"
+        recal_table="{sample}.recal_data_table",
     log:
-        "logs/gatk3/bqsr/{sample}.log"
+        "logs/gatk3/bqsr/{sample}.log",
     params:
-        extra=""  # optional
+        extra="--defaultBaseQualities 20 --filter_reads_with_N_cigar",  # optional
     resources:
-        mem_mb = 1024
+        mem_mb=1024,
     threads: 16
     wrapper:
-        "bio/gatk/baserecalibrator"
+        "master/bio/gatk3/baserecalibrator"

bio/gatk3/baserecalibrator/test/genome.dict

@@ -0,0 +1,3 @@
+@HD	VN:1.5
+@SQ	SN:ref	LN:45	M5:7a66cae8ab14aef8d635bc80649e730b	UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta
+@SQ	SN:ref2	LN:40	M5:1636753510ec27476fdd109a6684680e	UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta

bio/gatk3/baserecalibrator/test/genome.fasta

@@ -0,0 +1,4 @@
+>ref
+AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT
+>ref2
+aggttttataaaacaattaagtctacagagcaactacgcg

bio/gatk3/baserecalibrator/test/genome.fasta.fai

@@ -0,0 +1,2 @@
+ref	45	5	45	46
+ref2	40	57	40	41

bio/gatk3/baserecalibrator/wrapper.py

@@ -9,31 +9,31 @@
 from snakemake_wrapper_utils.java import get_java_opts
 
 extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 java_opts = get_java_opts(snakemake)
 
-input_bam = snakemake.input.bam
-input_known = snakemake.input.known
-input_ref = snakemake.input.ref
-bed = snakemake.params.get("bed", None)
-if bed is not None:
-    bed = "-L " + bed
-else:
-    bed = ""
 
-input_known_string = ""
-for known in input_known:
-    input_known_string = input_known_string + "  --knownSites {}".format(known)
+bed = snakemake.params.get("bed", "")
+if bed:
+    bed = f"--intervals {bed}"
+
+
+input_known = snakemake.input.get("known", "")
+if input_known:
+    if isinstance(input_known, str):
+        input_known = [input_known]
+    input_known = list(map("--knownSites {}".format, input_known))
 
-log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
 shell(
-    "gatk3 {java_opts} -T BaseRecalibrator"
-    " -nct {snakemake.threads}"
-    " {extra}"
-    " -I {input_bam}"
-    " -R {input_ref}"
-    " {input_known_string}"
+    "gatk3 {java_opts}"
+    " --analysis_type BaseRecalibrator"
+    " --num_cpu_threads_per_data_thread {snakemake.threads}"
+    " --input_file {snakemake.input.bam}"
+    " {input_known}"
+    " --reference_sequence {snakemake.input.ref}"
     " {bed}"
-    " -o {snakemake.output}"
+    " {extra}"
+    " --out {snakemake.output}"
     " {log}"
 )

bio/gatk3/indelrealigner/environment.yaml

@@ -3,5 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - gatk ==3.8
-  - snakemake-wrapper-utils ==0.1.3
+  - gatk =3.8
+  - python >=3.10
+  - snakemake-wrapper-utils =0.5

bio/gatk3/indelrealigner/test/Snakefile

@@ -1,21 +1,22 @@
 rule indelrealigner:
     input:
-        bam="mapped/{sample}.bam",
-        bai="mapped/{sample}.bai",
+        bam="{sample}.bam",
+        bai="{sample}.bai",
         ref="genome.fasta",
+        fai="genome.fasta.fai",
+        dict="genome.dict",
         known="dbsnp.vcf.gz",
         known_idx="dbsnp.vcf.gz.tbi",
-        target_intervals="{sample}.intervals"
+        target_intervals="{sample}.intervals",
     output:
-        bam="realigned/{sample}.bam",
-        bai="realigned/{sample}.bai",
-        java_temp=temp(directory("/tmp/gatk3_indelrealigner/{sample}")),
+        bam="{sample}.realigned.bam",
+        bai="{sample}.realigned.bai",
     log:
-        "logs/gatk3/indelrealigner/{sample}.log"
+        "logs/gatk3/indelrealigner/{sample}.log",
     params:
-        extra=""  # optional
+        extra="--defaultBaseQualities 20 --filter_reads_with_N_cigar",  # optional
     threads: 16
     resources:
-        mem_mb = 1024
+        mem_mb=1024,
     wrapper:
-        "bio/gatk/indelrealigner"
+        "master/bio/gatk3/indelrealigner"

bio/gatk3/indelrealigner/test/a.intervals

@@ -0,0 +1,2 @@
+ref:14-19
+ref2:14-15

bio/gatk3/indelrealigner/test/genome.dict

@@ -0,0 +1,3 @@
+@HD	VN:1.5
+@SQ	SN:ref	LN:45	M5:7a66cae8ab14aef8d635bc80649e730b	UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta
+@SQ	SN:ref2	LN:40	M5:1636753510ec27476fdd109a6684680e	UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta

bio/gatk3/indelrealigner/test/genome.fasta

@@ -0,0 +1,4 @@
+>ref
+AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT
+>ref2
+aggttttataaaacaattaagtctacagagcaactacgcg

bio/gatk3/indelrealigner/test/genome.fasta.fai

@@ -0,0 +1,2 @@
+ref	45	5	45	46
+ref2	40	57	40	41

bio/gatk3/indelrealigner/wrapper.py

@@ -10,38 +10,37 @@
 
 
 extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 java_opts = get_java_opts(snakemake)
 
 
 bed = snakemake.input.get("bed", "")
 if bed:
-    bed = "-L " + bed
+    bed = f"--intervals {bed}"
 
 
 known = snakemake.input.get("known", "")
 if known:
     if isinstance(known, str):
-        known = "-known {}".format(known)
+        known = f"--knownAlleles {known}"
     else:
-        known = list(map("-known {}".format, known))
+        known = list(map("----knownAlleles {}".format, known))
 
 
 output_bai = snakemake.output.get("bai", None)
 if output_bai is None:
     extra += " --disable_bam_indexing"
 
 
-log = snakemake.log_fmt_shell(stdout=True, stderr=True)
-
-
 shell(
-    "gatk3 {java_opts} -T IndelRealigner"
-    " {extra}"
-    " -I {snakemake.input.bam}"
-    " -R {snakemake.input.ref}"
+    "gatk3 {java_opts}"
+    " --analysis_type IndelRealigner"
+    " --input_file {snakemake.input.bam}"
+    " --reference_sequence {snakemake.input.ref}"
     " {known}"
     " {bed}"
     " --targetIntervals {snakemake.input.target_intervals}"
-    " -o {snakemake.output.bam}"
+    " {extra}"
+    " --out {snakemake.output.bam}"
     " {log}"
 )

bio/gatk3/printreads/environment.yaml

@@ -4,4 +4,5 @@ channels:
   - nodefaults
 dependencies:
   - gatk =3.8
+  - python >=3.10
   - snakemake-wrapper-utils =0.5.0

bio/gatk3/printreads/test/Snakefile

@@ -1,16 +1,20 @@
 rule printreads:
     input:
-        bam="mapped/{sample}.bam",
+        bam="{sample}.bam",
+        bai="{sample}.bai",
+#        recal_data="{sample}.recal_data_table",
         ref="genome.fasta",
-        recal_data="{sample}.recal_data_table"
+        fai="genome.fasta.fai",
+        dict="genome.dict",
     output:
-        "alignment/{sample}.bqsr.bam"
+        bam="{sample}.bqsr.bam",
+        bai="{sample}.bqsr.bai",
     log:
-        "logs/gatk/bqsr/{sample}..log"
+        "logs/gatk/bqsr/{sample}.log",
     params:
-        extra=""  # optional
+        extra="--defaultBaseQualities 20 --filter_reads_with_N_cigar",  # optional
     resources:
-        mem_mb = 1024
+        mem_mb=1024,
     threads: 16
     wrapper:
-        "bio/gatk3/printreads"
+        "master/bio/gatk3/printreads"