fix: issue when picard does not create output files (#496)

* Added touch to possibly missing files * Fixed typos * Bumped version * Remove append Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
snakemake · Jun 30, 2022 · aceab7e · aceab7e
1 parent 6419dbf
commit aceab7e
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Showing 20 changed files with 60 additions and 49 deletions.
diff --git a/bio/picard/addorreplacereadgroups/environment.yaml b/bio/picard/addorreplacereadgroups/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/bedtointervallist/environment.yaml b/bio/picard/bedtointervallist/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/collectalignmentsummarymetrics/environment.yaml b/bio/picard/collectalignmentsummarymetrics/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/collectgcbiasmetrics/environment.yaml b/bio/picard/collectgcbiasmetrics/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/collecthsmetrics/environment.yaml b/bio/picard/collecthsmetrics/environment.yaml
@@ -1,6 +1,7 @@
 channels:
   - bioconda
   - conda-forge
+  - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/collectinsertsizemetrics/environment.yaml b/bio/picard/collectinsertsizemetrics/environment.yaml
@@ -3,6 +3,6 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - r-base ==3.6.2
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/collectmultiplemetrics/environment.yaml b/bio/picard/collectmultiplemetrics/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/collectmultiplemetrics/meta.yaml b/bio/picard/collectmultiplemetrics/meta.yaml
@@ -1,54 +1,52 @@
 name: picard CollectMultipleMetrics
 description: >
   A ``picard`` meta-metrics tool that collects multiple classes of metrics.
-  For usage information about CollectMultipleMetrics, please see  ``picard``'s `documentation <https://broadinstitute.github.io/picard/command-line-overview.html#CollectMultipleMetrics>`_.
-  For more information about ``picard``, also see the `source code <https://github.com/broadinstitute/picard>`_.
-
 
   You can select which tool(s) to run by adding the respective extension(s) (see table below) to the requested output of the wrapper invocation (see example Snakemake rule below).
 
     +-----------------------------------+-----------------------------------------+
     |               Tool                |    Extension(s) for the output files    |
     +===================================+=========================================+
-    | CollectAlignmentSummaryMetrics    | ".alignment_summary_metrics"            |
+    | CollectAlignmentSummaryMetrics    | `.alignment_summary_metrics`            |
     +-----------------------------------+-----------------------------------------+
-    | CollectInsertSizeMetrics          | ".insert_size_metrics",                 |
+    | CollectInsertSizeMetrics          | `.insert_size_metrics`,                 |
     |                                   |                                         |
-    |                                   | ".insert_size_histogram.pdf"            |
+    |                                   | `.insert_size_histogram.pdf`            |
     +-----------------------------------+-----------------------------------------+
-    | QualityScoreDistribution          | ".quality_distribution_metrics",        |
+    | QualityScoreDistribution          | `.quality_distribution_metrics`,        |
     |                                   |                                         |
-    |                                   | ".quality_distribution.pdf"             |
+    |                                   | `.quality_distribution.pdf`             |
     +-----------------------------------+-----------------------------------------+
-    | MeanQualityByCycle                | ".quality_by_cycle_metrics",            |
+    | MeanQualityByCycle                | `.quality_by_cycle_metrics`,            |
     |                                   |                                         |
-    |                                   | ".quality_by_cycle.pdf"                 |
+    |                                   | `.quality_by_cycle.pdf`                 |
     +-----------------------------------+-----------------------------------------+
-    | CollectBaseDistributionByCycle    | ".base_distribution_by_cycle_metrics",  |
+    | CollectBaseDistributionByCycle    | `.base_distribution_by_cycle_metrics`,  |
     |                                   |                                         |
-    |                                   | ".base_distribution_by_cycle.pdf"       |
+    |                                   | `.base_distribution_by_cycle.pdf`       |
     +-----------------------------------+-----------------------------------------+
-    | CollectGcBiasMetrics              | ".gc_bias.detail_metrics",              |
+    | CollectGcBiasMetrics              | `.gc_bias.detail_metrics`,              |
     |                                   |                                         |
-    |                                   | ".gc_bias.summary_metrics",             |
+    |                                   | `.gc_bias.summary_metrics`,             |
     |                                   |                                         |
-    |                                   | ".gc_bias.pdf"                          |
+    |                                   | `.gc_bias.pdf`                          |
     +-----------------------------------+-----------------------------------------+
-    | RnaSeqMetrics                     | ".rna_metrics"                          |
+    | RnaSeqMetrics                     | `.rna_metrics`                          |
     +-----------------------------------+-----------------------------------------+
-    | CollectSequencingArtifactMetrics  | ".bait_bias_detail_metrics",            |
+    | CollectSequencingArtifactMetrics  | `.bait_bias_detail_metrics`,            |
     |                                   |                                         |
-    |                                   | ".bait_bias_summary_metrics",           |
+    |                                   | `.bait_bias_summary_metrics`,           |
     |                                   |                                         |
-    |                                   | ".error_summary_metrics",               |
+    |                                   | `.error_summary_metrics`,               |
     |                                   |                                         |
-    |                                   | ".pre_adapter_detail_metrics",          |
+    |                                   | `.pre_adapter_detail_metrics`,          |
     |                                   |                                         |
-    |                                   | ".pre_adapter_summary_metrics"          |
+    |                                   | `.pre_adapter_summary_metrics`          |
     +-----------------------------------+-----------------------------------------+
-    | CollectQualityYieldMetrics        | ".quality_yield_metrics"                |
+    | CollectQualityYieldMetrics        | `.quality_yield_metrics`                |
     +-----------------------------------+-----------------------------------------+
 
+url: https://broadinstitute.github.io/picard/command-line-overview.html#CollectMultipleMetrics
 authors:
   - David Laehnemann
   - Antonie Vietor
@@ -61,7 +59,6 @@ output:
   - multiple metrics pdf files (.pdf)
   - the appropriate extensions for the output files must be used depending on the desired tools
 notes: |
-  * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).
+  * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. `-XX:ParallelGCThreads=10` (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).
   * The `extra` param allows for additional program arguments.
   * `--TMP_DIR` is automatically set by `resources.tmpdir`
-  * For more information see, https://broadinstitute.github.io/picard/command-line-overview.html#CollectMultipleMetrics
diff --git a/bio/picard/collectmultiplemetrics/wrapper.py b/bio/picard/collectmultiplemetrics/wrapper.py
@@ -3,12 +3,12 @@
 __email__ = "antonie.v@gmx.de"
 __license__ = "MIT"
 
-import sys
 import tempfile
+from pathlib import Path
 from snakemake.shell import shell
 from snakemake_wrapper_utils.java import get_java_opts
 
-log = snakemake.log_fmt_shell(stdout=False, stderr=True)
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
 extra = snakemake.params.get("extra", "")
 java_opts = get_java_opts(snakemake)
@@ -34,28 +34,32 @@
     ".pre_adapter_summary_metrics": "CollectSequencingArtifactMetrics",
     ".quality_yield_metrics": "CollectQualityYieldMetrics",
 }
-progs = set()
 
+
+# Select programs to run from output files
+progs = set()
 for file in snakemake.output:
     matched = False
     for ext in exts_to_prog:
         if file.endswith(ext):
             progs.add(exts_to_prog[ext])
             matched = True
     if not matched:
-        sys.exit(
+        raise ValueError(
             "Unknown type of metrics file requested, for possible metrics files, see https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/picard/collectmultiplemetrics.html"
         )
 
-programs = " --PROGRAM null --PROGRAM " + " --PROGRAM ".join(progs)
+programs = "--PROGRAM null --PROGRAM " + " --PROGRAM ".join(progs)
+
 
-out = str(snakemake.wildcards.sample)  # as default
+# Infer common output prefix
 output_file = str(snakemake.output[0])
 for ext in exts_to_prog:
     if output_file.endswith(ext):
         out = output_file[: -len(ext)]
         break
 
+
 with tempfile.TemporaryDirectory() as tmpdir:
     shell(
         "picard CollectMultipleMetrics"
@@ -67,3 +71,12 @@
         " {programs}"
         " {log}"
     )
+
+
+# Under some circumstances, some picard programs might not produce an output (https://github.com/snakemake/snakemake-wrappers/issues/357). To avoid snakemake errors, the output files of those programs are created empty (if they do not exist).
+for ext in [
+    ext for ext, prog in exts_to_prog.items() if prog in ["CollectInsertSizeMetrics"]
+]:
+    for file in snakemake.output:
+        if file.endswith(ext) and not Path(file).is_file():
+            Path(file).touch()
diff --git a/bio/picard/collectrnaseqmetrics/environment.yaml b/bio/picard/collectrnaseqmetrics/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/collecttargetedpcrmetrics/environment.yaml b/bio/picard/collecttargetedpcrmetrics/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/createsequencedictionary/environment.yaml b/bio/picard/createsequencedictionary/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/markduplicates/environment.yaml b/bio/picard/markduplicates/environment.yaml
@@ -3,6 +3,6 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
-  - samtools =1.15.1
+  - picard =2.27
+  - samtools =1.15
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/markduplicateswithmatecigar/environment.yaml b/bio/picard/markduplicateswithmatecigar/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/markduplicateswithmatecigar/wrapper.py b/bio/picard/markduplicateswithmatecigar/wrapper.py
@@ -8,7 +8,7 @@
 from snakemake.shell import shell
 from snakemake_wrapper_utils.java import get_java_opts
 
-log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
 extra = snakemake.params.get("extra", "")
 java_opts = get_java_opts(snakemake)

diff --git a/bio/picard/mergesamfiles/environment.yaml b/bio/picard/mergesamfiles/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/mergevcfs/environment.yaml b/bio/picard/mergevcfs/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/revertsam/environment.yaml b/bio/picard/revertsam/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/samtofastq/environment.yaml b/bio/picard/samtofastq/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/picard/sortsam/environment.yaml b/bio/picard/sortsam/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - picard =2.26
+  - picard =2.27
   - snakemake-wrapper-utils ==0.1.3