Fixes sequana#31 and sequana#15

environment.yml

@@ -7,6 +7,8 @@ channels:
 - r
 
 dependencies:
+- cutadapt
+- atropos
 - bowtie
 - samtools>1.7
 - bamtools

requirements.txt

@@ -1,2 +1,4 @@
 sequana>=0.14.2
 sequana_pipetools>=0.9.2
+cutadapt
+atropos

sequana_pipelines/rnaseq/config.yaml

@@ -7,6 +7,8 @@
 # If input_directory provided, use it otherwise if input_pattern provided,
 # use it, otherwise use input_samples.
 # ============================================================================
+sequana_wrappers: "v0.15.1"
+
 input_directory:
 input_readtag: _R[12]_
 input_pattern: '*fastq.gz'
@@ -45,14 +47,6 @@ general:
     custom_gff: ''
 
 
-######################
-# if files are required for a pipeline and are within sequana or should
-# be downloaded before the pipeline provide them in this section
-# Note that sequana and url fields are followed by itemised files or links
-# using the front dashes
-requirements: ''
-
-
 #################################################################
 # FastQC section
 #

sequana_pipelines/rnaseq/main.py

@@ -67,9 +67,16 @@ def __init__(self, prog=NAME, epilog=None):
         )
         pipeline_group.add_argument(
             "--rRNA-feature",
+            action="store_true",
             default="rRNA",
             help="""Feature name corresponding to the rRNA to be identified in
-the input GFF/GTF files""",
+the input GFF/GTF files. Must exist and be valid. If you do not have any, 
+you may skip this step using --skip-rRNA or provide a fasta file using --contaminant-file""",
+        )
+        pipeline_group.add_argument(
+            "--skip-rRNA",
+            action="store_true",
+            help="""skip the mapping on rRNA feature. ignored if --contaminant-file is provided""",
         )
         pipeline_group.add_argument(
             "--contaminant-file",
@@ -208,6 +215,8 @@ def main(args=None):
                 "You are using a custom FASTA --contaminant_file so --rRNA-feature will be ignored"
             )
             cfg.general.rRNA_feature = None
+        elif options.skip_rRNA:
+            cfg.general.rRNA_feature = None
         else:
             cfg.general.rRNA_feature = options.rRNA_feature