Added minimum_envs folder and contents

For commands and resources to update envs when needed

resources/minimum_envs/.README

@@ -0,0 +1,8 @@
+This folder contains the minimum tools required for each MOSCA environment.
+
+When updating a new environment, the following commands should be run from this directory, assigning the correct value for the `ENV_NAME` variable:
+`bash
+ENV_NAME=env_name
+mamba create $ENV_NAME.yml
+mamba env export --from-history -f $ENV_NAME.yml > $ENV_NAME.yml
+`

resources/minimum_envs/assembly.yaml

@@ -0,0 +1,13 @@
+name: assembly
+channels:
+  - conda-forge
+  - bioconda
+  - anaconda
+  - defaults
+dependencies:
+  - bowtie2
+  - gmcloser
+  - megahit
+  - quast
+  - samtools
+  - spades

resources/minimum_envs/binning.yaml

@@ -0,0 +1,9 @@
+name: binning
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - checkm-genome
+  - maxbin2
+  - pandas

resources/minimum_envs/de_analysis.yaml

@@ -0,0 +1,15 @@
+name: de_analysis
+channels:
+  - conda-forge
+  - bioconda
+  - anaconda
+  - defaults
+dependencies:
+  - bioconductor-annotationdbi      # check if needed
+  - bioconductor-deseq2
+  - bioconductor-genomeinfodb
+  - bioconductor-genomeinfodbdata   # check if needed
+  - bioconductor-genomicranges      # check if needed
+  - bioconductor-rots
+  - r-base=4                        # check if needed
+  - r-pheatmap

resources/minimum_envs/gene_calling.yaml

@@ -0,0 +1,7 @@
+name: gene_calling
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - fraggenescan

resources/minimum_envs/keggcharter.yaml

@@ -0,0 +1,8 @@
+name: keggcharter
+channels:
+  - conda-forge
+  - bioconda
+  - anaconda
+  - defaults
+dependencies:
+  - keggcharter>=1.1.2

resources/minimum_envs/metaproteomics.yaml

@@ -0,0 +1,9 @@
+name: metaproteomics
+channels:
+  - conda-forge
+  - bioconda
+  - anaconda
+  - defaults
+dependencies:
+  - peptide-shaker=2
+  - searchgui=4

resources/minimum_envs/normalization.yaml

@@ -0,0 +1,11 @@
+name: normalization
+channels:
+  - conda-forge
+  - bioconda
+  - anaconda
+  - defaults
+dependencies:
+  - bioconductor-limma          # check if needed
+  - bioconductor-pcamethods
+  - bioconductor-vsn
+  - r-base=4                    # check if needed

resources/minimum_envs/preprocess.yaml

@@ -0,0 +1,11 @@
+name: preprocess
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - fastqc
+  - pandas
+  - numpy
+  - sortmerna=4
+  - trimmomatic=0.39

resources/minimum_envs/quantification.yaml

@@ -0,0 +1,11 @@
+name: quantification
+channels:
+  - conda-forge
+  - bioconda
+  - anaconda
+  - defaults
+dependencies:
+  - bowtie2
+  - numpy
+  - pandas
+  - samtools

resources/minimum_envs/recognizer.yaml

@@ -0,0 +1,8 @@
+name: recognizer
+channels:
+  - conda-forge
+  - bioconda
+  - anaconda
+  - defaults
+dependencies:
+  - recognizer>=1.10.1

resources/minimum_envs/reports.yaml

@@ -0,0 +1,12 @@
+name: reports
+channels:
+  - conda-forge
+  - bioconda
+  - anaconda
+  - defaults
+dependencies:
+  - numpy
+  - openpyxl
+  - pandas
+  - tqdm
+  - xlsxwriter

resources/minimum_envs/seqkit.yaml

@@ -0,0 +1,6 @@
+name: seqkit
+channels:
+  - bioconda
+  - defaults
+dependencies:
+  - seqkit

resources/minimum_envs/summary.yaml

@@ -0,0 +1,9 @@
+name: summary
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - numpy
+  - openpyxl
+  - pandas
+  - tqdm

resources/minimum_envs/upimapi.yaml

@@ -0,0 +1,8 @@
+name: upimapi
+channels:
+  - conda-forge
+  - bioconda
+  - anaconda
+  - defaults
+dependencies:
+  - upimapi>=1.13.1

workflow/scripts/preprocess.py

@@ -9,10 +9,8 @@
 March 2017
 '''
 
-import argparse
 import shutil
 from glob import glob
-from multiprocessing import cpu_count
 import os
 import pathlib
 import time