Updating biopython+numpy images built with anaconda to biopython wo a…

…naconda
sanger-tol · Nov 26, 2024 · 302c18e · 302c18e
1 parent 7aac083
commit 302c18e
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Showing 5 changed files with 88 additions and 37 deletions.
diff --git a/bin/trim_Ns.py b/bin/trim_Ns.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python
 """
-Script for detecting trailing Ns that should be trimmed from an assembly, from James Torrance ([email protected]). Edited by Eerik Aunin ([email protected])
+Script for detecting trailing Ns that should be trimmed from an assembly,
+Written by James Torrance ([email protected]).
+Edited by Eerik Aunin ([email protected])
 """
 
 import re
@@ -43,9 +45,11 @@ def main(fasta_file, output_file):
             startseq = ""
             if start_n_match:
                 startseq = start_n_match.group(1)
+
             endseq = ""
             if end_n_match:
                 endseq = end_n_match.group(1)
+
             realseq_length = len(seq_string) - len(startseq) - len(endseq)
             # Handle "all Ns exception"
             if len(startseq) == len(seq_string):
@@ -85,7 +89,7 @@ def main(fasta_file, output_file):
 
                         # Does the *end* of this block satisfy the window condition?
                         bases_in_window = 0
-                        start_of_first_base_block_in_window = None
+                        start_of_first_base_block_in_window = 0 # Replacement of the None assignment with 0 to apease the linting gods
                         for non_n_region in non_n_regions:
                             if non_n_region[1] >= current_non_n_end - winsize:
                                 start_of_first_base_block_in_window = non_n_region[0]

diff --git a/modules.json b/modules.json
@@ -8,109 +8,151 @@
                     "blast/blastn": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "blast/makeblastdb": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/blast/makeblastdb/blast-makeblastdb.diff"
                     },
                     "custom/getchromsizes": {
                         "branch": "master",
                         "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/custom/getchromsizes/custom-getchromsizes.diff"
                     },
                     "diamond/blastx": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "21f230b8cca43755bf73470e6fd0290832a98aef",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fcs/fcsadaptor": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fcs/fcsgx": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gnu/sort": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "minimap2/align": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "minimap2/index": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "ncbitools/vecscreen": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/depth": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/faidx": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/merge": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/sort": {
                         "branch": "master",
                         "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/view": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "seqkit/sliding": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "tiara/tiara": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             },
@@ -119,20 +161,26 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/modules/local/chunk_assembly_for_vecscreen.nf b/modules/local/chunk_assembly_for_vecscreen.nf
@@ -2,10 +2,10 @@ process CHUNK_ASSEMBLY_FOR_VECSCREEN {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::biopython=1.70"
+    conda "bioconda::biopython=1.81"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/biopython:1.70--np112py35_1':
-        'quay.io/biocontainers/biopython:1.70--np112py35_1' }"
+        'https://depot.galaxyproject.org/singularity/biopython:1.81':
+        'quay.io/biocontainers/biopython:1.81' }"
 
     input:
     tuple val(meta), path(fasta_input_file)

diff --git a/modules/local/trailingns.nf b/modules/local/trailingns.nf
@@ -2,9 +2,10 @@ process TRAILINGNS {
     tag "$meta.id"
     label 'process_single'
 
+    conda "bioconda::biopython=1.81"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/biopython:1.70--np112py27_1':
-        'biocontainers/biopython:1.70--np112py27_1' }"
+        'https://depot.galaxyproject.org/singularity/biopython:1.81':
+        'quay.io/biocontainers/biopython:1.81' }"
 
     input:
     tuple val(meta), path(fasta_input_file)

diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml