Merge pull request #24 from U-BDS/dev

Documentation and linting

bin/config.py

@@ -1,3 +1,13 @@
+"""
+This is modified script from the `support-5prim-kit` branch of the BLAZE repo, link below:
+https://github.com/shimlab/BLAZE/tree/support-5prim-kit
+
+The only modifications that have been made are formatting changes in order to meet the
+nf-core linting requirements. The script has been copied into the pipeline temporarily
+in order to support 5-prime data, and will be removed once this feature has been
+incorporated into an official BLAZE release.
+"""
+
 # This file stores the parameter used in this repo
 
 import os

bin/find_reads.py

@@ -1,3 +1,13 @@
+"""
+This is modified script from the `support-5prim-kit` branch of the BLAZE repo, link below:
+https://github.com/shimlab/BLAZE/tree/support-5prim-kit
+
+The only modifications that have been made are formatting changes in order to meet the
+nf-core linting requirements. The script has been copied into the pipeline temporarily
+in order to support 5-prime data, and will be removed once this feature has been
+incorporated into an official BLAZE release.
+"""
+
 # find specific reads with given read id and output to a new fastq file
 
 

bin/helper.py

@@ -1,3 +1,13 @@
+"""
+This is modified script from the `support-5prim-kit` branch of the BLAZE repo, link below:
+https://github.com/shimlab/BLAZE/tree/support-5prim-kit
+
+The only modifications that have been made are formatting changes in order to meet the
+nf-core linting requirements. The script has been copied into the pipeline temporarily
+in order to support 5-prime data, and will be removed once this feature has been
+incorporated into an official BLAZE release.
+"""
+
 import numpy as np
 import pandas as pd
 import concurrent.futures

bin/main.py

@@ -1,6 +1,14 @@
 #!/usr/bin/env python3
 
 """
+This is modified script from the `support-5prim-kit` branch of the BLAZE repo, link below:
+https://github.com/shimlab/BLAZE/tree/support-5prim-kit
+
+The only modifications that have been made are formatting changes in order to meet the
+nf-core linting requirements. The script has been copied into the pipeline temporarily
+in order to support 5-prime data, and will be removed once this feature has been
+incorporated into an official BLAZE release.
+
 Get raw BC (i.e. putative barcode) from fastq file
 
 Output:

bin/polyT_adaptor_finder.py

@@ -1,4 +1,13 @@
-"""Searching for adaptor polyT or poly A in a Nanopore read.
+"""
+This is modified script from the `support-5prim-kit` branch of the BLAZE repo, link below:
+https://github.com/shimlab/BLAZE/tree/support-5prim-kit
+
+The only modifications that have been made are formatting changes in order to meet the
+nf-core linting requirements. The script has been copied into the pipeline temporarily
+in order to support 5-prime data, and will be removed once this feature has been
+incorporated into an official BLAZE release.
+
+Searching for adaptor polyT or poly A in a Nanopore read.
 """
 import numpy as np
 from fast_edit_distance import sub_edit_distance

bin/polyT_trimmer.py

@@ -1,3 +1,13 @@
+"""
+This is modified script from the `support-5prim-kit` branch of the BLAZE repo, link below:
+https://github.com/shimlab/BLAZE/tree/support-5prim-kit
+
+The only modifications that have been made are formatting changes in order to meet the
+nf-core linting requirements. The script has been copied into the pipeline temporarily
+in order to support 5-prime data, and will be removed once this feature has been
+incorporated into an official BLAZE release.
+"""
+
 from collections import namedtuple
 import argparse
 from tqdm import tqdm

bin/read_assignment.py

@@ -1,3 +1,13 @@
+"""
+This is modified script from the `support-5prim-kit` branch of the BLAZE repo, link below:
+https://github.com/shimlab/BLAZE/tree/support-5prim-kit
+
+The only modifications that have been made are formatting changes in order to meet the
+nf-core linting requirements. The script has been copied into the pipeline temporarily
+in order to support 5-prime data, and will be removed once this feature has been
+incorporated into an official BLAZE release.
+"""
+
 from fast_edit_distance import edit_distance, sub_edit_distance
 import multiprocessing as mp
 import tempfile

bin/update_whitelist.py

@@ -1,3 +1,14 @@
+"""
+This is modified script from the `support-5prim-kit` branch of the BLAZE repo, link below:
+https://github.com/shimlab/BLAZE/tree/support-5prim-kit
+
+The only modifications that have been made are formatting changes in order to meet the
+nf-core linting requirements. The script has been copied into the pipeline temporarily
+in order to support 5-prime data, and will be removed once this feature has been
+incorporated into an official BLAZE release.
+
+"""
+
 # Generate new whitelist from baw_bc table
 
 import argparse

conf/modules.config

@@ -192,7 +192,7 @@ if (!params.skip_qc){
             ]
         }
     }
-    
+
     process {
         withName:'.*:BAM_SORT_STATS_SAMTOOLS_DEDUP:BAM_STATS_SAMTOOLS:.*' {
             ext.prefix = { "${meta.id}.dedup.sorted" }

modules/local/blaze.nf

@@ -5,7 +5,9 @@ process BLAZE {
 
     conda "atrull314::fast_edit_distance=1.2.1 conda-forge::matplotlib=3.8.4 conda-forge::biopython=1.83 conda-forge::pandas=2.2.2 conda-forge::numpy=2.0.0rc2 conda-forge::tqdm=4.66.4"
 
-    container "docker://agtrull314/blaze_test:2.2.0"
+    container "${ workflow.containerEngine == 'singularity' ?
+        'docker://agtrull314/blaze:2.2.0' :
+        'docker.io/agtrull314/blaze:2.2.0'}"
 
     input:
     tuple val(meta), path(reads)