feat: make it possible to set input as files or dirs to multiqc

bio/multiqc/meta.yaml

@@ -1,9 +1,12 @@
 name: multiqc
 description: |
   Generate qc report using multiqc.
+url: https://multiqc.info/
 authors:
   - Julian de Ruiter
 input:
-  - input directory containing qc files
+  - input directory containing qc files, default behaviour is to extract folder path from the provided files or parent folder if a folder is provided.
+params:
+  - use_input_files_only: if this variable is set to True input will be used as it is, i.e no folder will be extract from provided file names
 output:
   - qc report (html)

bio/multiqc/test/Snakefile

@@ -1,10 +1,23 @@
-rule multiqc:
+rule multiqc_dir:
     input:
         expand("samtools_stats/{sample}.txt", sample=["a", "b"])
     output:
         "qc/multiqc.html"
     params:
-        ""  # Optional: extra parameters for multiqc.
+        extra=""  # Optional: extra parameters for multiqc.
+    log:
+        "logs/multiqc.log"
+    wrapper:
+        "master/bio/multiqc"
+
+rule multiqc_file:
+    input:
+        expand("samtools_stats/{sample}.txt", sample=["a"])
+    output:
+        "qc/multiqc_a.html"
+    params:
+        extra="",  # Optional: extra parameters for multiqc.
+        use_input_files_only=True, # Optional, use only a.txt and don't search folder samtools_stats for files
     log:
         "logs/multiqc.log"
     wrapper:

bio/multiqc/wrapper.py

@@ -11,17 +11,26 @@
 from snakemake.shell import shell
 
 
-input_dirs = set(path.dirname(fp) for fp in snakemake.input)
+extra = snakemake.params.get("extra", "")
+# Set this to False if multiqc should use the actual input directly
+# instead of parsing the folders where the provided files are located
+use_input_files_only = snakemake.params.get("use_input_files_only", False)
+
+if not use_input_files_only:
+    input_data = set(path.dirname(fp) for fp in snakemake.input)
+else:
+    input_data = set(snakemake.input)
+
 output_dir = path.dirname(snakemake.output[0])
 output_name = path.basename(snakemake.output[0])
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
 shell(
     "multiqc"
-    " {snakemake.params}"
+    " {extra}"
     " --force"
     " -o {output_dir}"
     " -n {output_name}"
-    " {input_dirs}"
+    " {input_data}"
     " {log}"
 )

test.py

@@ -2052,6 +2052,12 @@ def test_multiqc():
         ["snakemake", "--cores", "1", "qc/multiqc.html", "--use-conda", "-F"],
     )
 
+@skip_if_not_modified
+def test_multiqc_a():
+    run(
+        "bio/multiqc",
+        ["snakemake", "--cores", "1", "qc/multiqc_a.html", "--use-conda", "-F"],
+    )
 
 @skip_if_not_modified
 def test_muscle_clw():