fix: Nextflow profile (#456)

* Update wrapper.py

Fix
ERROR: You used a core Nextflow option with two hyphens: '--profile'. Please resubmit with '-profi
le'

WARN: Found unexpected parameters:
* --profile: [singularity]

nextflow run nf-core/mag -revision 2.1.1 -profile singularity --input output/SRR13435231.csv --profile ['singularity']

* Update wrapper.py

* Update environment.yaml

* Update wrapper.py

Added extra parameter to accommodate additional workflow flags.

* Update wrapper.py

* black formatting

* Update wrapper.py

Fix
ERROR: You used a core Nextflow option with two hyphens: '--profile'. Please resubmit with '-profi
le'

WARN: Found unexpected parameters:
* --profile: [singularity]

nextflow run nf-core/mag -revision 2.1.1 -profile singularity --input output/SRR13435231.csv --profile ['singularity']

* Update wrapper.py

* Update environment.yaml

* Update wrapper.py

Added extra parameter to accommodate additional workflow flags.

* Update wrapper.py

* black formatting

utils/nextflow/environment.yaml

@@ -2,4 +2,4 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - nextflow =20.10
+  - nextflow

utils/nextflow/wrapper.py

@@ -8,6 +8,7 @@
 
 revision = snakemake.params.get("revision")
 profile = snakemake.params.get("profile", [])
+extra = snakemake.params.get("extra", "")
 if isinstance(profile, str):
     profile = [profile]
 
@@ -31,11 +32,16 @@
         files = ",".join(files)
     add_parameter(name, files)
 for name, value in snakemake.params.items():
-    if name != "pipeline" and name != "revision":
+    if (
+        name != "pipeline"
+        and name != "revision"
+        and name != "profile"
+        and name != "extra"
+    ):
         add_parameter(name, value)
 
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 args = " ".join(args)
 pipeline = snakemake.params.pipeline
 
-shell("nextflow run {pipeline} {args} {log}")
+shell("nextflow run {pipeline} {args} {extra} {log}")