uses local conda to sidestep wrapper's - #47

configs/env/multiqc.yaml

 channels:
-  - conda-forge
-  - anaconda
   - bioconda
+  - conda-forge
+  - defaults
 dependencies:
   - python =3.6
-  - multiqc=1.9
+  - multiqc ==1.9

src/wrapper_edited/0.64.0_bio_multiqc/environment.yaml

-channels:
-  - bioconda
-  - conda-forge
-  - defaults
-dependencies:
-  - python =3.6
-  - multiqc ==1.9

src/wrapper_edited/0.64.0_bio_multiqc/meta.yaml

-name: multiqc
-description: |
-  Generate qc report using multiqc.
-authors:
-  - Julian de Ruiter
-input:
-  - input directory containing qc files
-output:
-  - qc report (html)

src/wrapper_edited/0.64.0_bio_multiqc/wrapper.py

-"""Snakemake wrapper for trimming paired-end reads using cutadapt."""
-
-__author__ = "Julian de Ruiter"
-__copyright__ = "Copyright 2017, Julian de Ruiter"
-__email__ = "julianderuiter@gmail.com"
-__license__ = "MIT"
-
-
-from os import path
-
-from snakemake.shell import shell
-
-
-input_dirs = set(path.dirname(fp) for fp in 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}"
-    " --force"
-    " -o {output_dir}"
-    " -n {output_name}"
-    " {input_dirs}"
-    " {log}"
-)

workflow/rules/aggregate_results.smk

@@ -50,10 +50,11 @@ rule multiqc_by_sample_initial_pass:
         # multiqc uses fastq's filenames to identify sample names. Rename them to in-house names,
         # using custom rename config file
         extra=lambda wildcards, input: f"--config {input.multiqc_config} --sample-names {input.rename_config}",
+    conda:
+        ### see issue #47 on why local conda env is used to sidestep snakemake-wrapper's ###
+        str(WORKFLOW_PATH / "configs/env/multiqc.yaml")
     wrapper:
-        # "0.64.0/bio/multiqc"
-        ### see issue #47 on why local wrapper is used ###
-        "file:src/wrapper_edited/0.64.0_bio_multiqc/wrapper.py"
+        "0.64.0/bio/multiqc"
 
 
 rule quac_watch:
@@ -135,10 +136,11 @@ rule multiqc_by_sample_final_pass:
         # multiqc uses fastq's filenames to identify sample names. Rename them to in-house names,
         # using custom rename config file
         extra=lambda wildcards, input: f"--config {input.multiqc_config} --sample-names {input.rename_config}",
+    conda:
+        ### see issue #47 on why local conda env is used to sidestep snakemake-wrapper's ###
+        str(WORKFLOW_PATH / "configs/env/multiqc.yaml")
     wrapper:
-        # "0.64.0/bio/multiqc"
-        ### see issue #47 on why local wrapper is used ###
-        "file:src/wrapper_edited/0.64.0_bio_multiqc/wrapper.py"
+        "0.64.0/bio/multiqc"
 
 
 
@@ -197,8 +199,8 @@ rule multiqc_aggregation_all_samples:
                                             --sample-names {input.rename_config} \
                                             --cl_config "max_table_rows: 2000"'
         ),
+    conda:
+        ### see issue #47 on why local conda env is used to sidestep snakemake-wrapper's ###
+        str(WORKFLOW_PATH / "configs/env/multiqc.yaml")
     wrapper:
-        # "0.64.0/bio/multiqc"
-        ### see issue #47 on why local wrapper is used ###
-        "file:src/wrapper_edited/0.64.0_bio_multiqc/wrapper.py"
-
+        "0.64.0/bio/multiqc"