separate env for fq lint

Author: WardDeb

.github/workflows/linux.yml

@@ -100,7 +100,8 @@ jobs:
           'CONDA_PREPROCESSING_ENV',
           'CONDA_NONCODING_RNASEQ_ENV',
           'CONDA_SAMBAMBA_ENV',
-          'CONDA_pysam_ENV'
+          'CONDA_pysam_ENV',
+          'CONDA_FQLINT_ENV'
         ]
     runs-on: ubuntu-latest
     steps:

.github/workflows/osx.yml

@@ -31,7 +31,8 @@ jobs:
           'CONDA_PREPROCESSING_ENV',
           'CONDA_NONCODING_RNASEQ_ENV',
           'CONDA_SAMBAMBA_ENV',
-          'CONDA_pysam_ENV'
+          'CONDA_pysam_ENV',
+          'CONDA_FQLINT_ENV'
         ]
     runs-on: macos-latest
     steps:

snakePipes/common_functions.py

@@ -42,7 +42,9 @@ def set_env_yamls():
             'CONDA_NONCODING_RNASEQ_ENV': 'envs/noncoding.yaml',
             'CONDA_SAMBAMBA_ENV': 'envs/sambamba.yaml',
             'CONDA_pysam_ENV': 'envs/pysam.yaml',
-            'CONDA_SEACR_ENV': 'envs/chip_seacr.yaml'}
+            'CONDA_SEACR_ENV': 'envs/chip_seacr.yaml',
+            'CONDA_FQLINT_ENV': 'envs/fqlint.yaml'
+            }
 
 
 def merge_dicts(x, y):

snakePipes/shared/rules/FASTQ.snakefile

@@ -5,7 +5,7 @@ if pairedEnd or pipeline=="scrnaseq":
             r2 = indir+"/{sample}"+reads[1]+ext
         output:
             temp("originalFASTQ/{sample}.valid")
-        conda: CONDA_SHARED_ENV
+        conda: CONDA_FQLINT_ENV
         shell:"""
             fq lint {input.r1} {input.r2}
             touch {output}
@@ -16,7 +16,7 @@ else:
             r1 = indir+"/{sample}"+reads[0]+ext
         output:
             temp("originalFASTQ/{sample}.valid")
-        conda: CONDA_SHARED_ENV
+        conda: CONDA_FQLINT_ENV
         shell:"""
             fq lint {input.r1}
             touch {output}

snakePipes/shared/rules/envs/fqlint.yaml

@@ -0,0 +1,4 @@
+channels:
+ - bioconda
+dependencies:
+ - fq = 0.12.0

snakePipes/shared/rules/envs/shared.yaml

@@ -1,7 +1,7 @@
 name: snakepipes_shared_environment_2.0
 channels:
- - bioconda
  - conda-forge
+ - bioconda
 dependencies:
  - python = 3.10.13
  - deeptools = 3.5.4
@@ -15,6 +15,5 @@ dependencies:
  - multiqc = 1.23
  - fastp = 0.23.4
  - umi_tools = 1.1.4
- - fq = 0.12.0
  - pybigwig = 0.3.22