From 20b71fa0880ef3d870e4c3c5bf5375054852fd98 Mon Sep 17 00:00:00 2001
From: Matthew Wells <mattwells9@shaw.ca>
Date: Thu, 11 Jul 2024 13:48:32 -0500
Subject: [PATCH 1/8] dropped quay.io from docker paths

---
 nextflow.config | 76 +++++++++++++++++++++++++++----------------------
 1 file changed, 42 insertions(+), 34 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index f6675468..b8d445ca 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -173,7 +173,7 @@ params {
 
     abricate {
         singularity = "https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1"
-        docker = "quay.io/biocontainers/abricate:1.0.1--ha8f3691_1"
+        docker = "biocontainers/abricate:1.0.1--ha8f3691_1"
         args = { "" }
         report_tag = "Abricate"
         header_p = true
@@ -188,18 +188,18 @@ params {
     // coreutils e.g. cat
     coreutils {
         singularity = "https://depot.galaxyproject.org/singularity/coreutils%3A8.31--h14c3975_0"
-        docker = 'quay.io/biocontainers/coreutils:8.31--h14c3975_0'
+        docker = 'biocontainers/coreutils:8.31--h14c3975_0'
     }
 
     // Python container, May switch for pypy3
     python3 {
-        singularity = "quay.io/biocontainers/staramr:0.10.0--pyhdfd78af_0"
-        docker = "quay.io/biocontainers/staramr:0.10.0--pyhdfd78af_0"
+        singularity = "biocontainers/staramr:0.10.0--pyhdfd78af_0"
+        docker = "biocontainers/staramr:0.10.0--pyhdfd78af_0"
     }
 
     seqtk {
         singularity = 'https://depot.galaxyproject.org/singularity/seqtk%3A1.4--he4a0461_1'
-        docker = 'quay.io/biocontainers/seqtk:1.4--he4a0461_1'
+        docker = 'biocontainers/seqtk:1.4--he4a0461_1'
         seed = 42
         reads_ext = ".sampled.fastq.gz"
         assembly_fastq = ".fastq.gz"
@@ -208,15 +208,15 @@ params {
 
     seqtk_size {
         singularity = 'https://depot.galaxyproject.org/singularity/seqtk%3A1.4--he4a0461_1'
-        docker = 'quay.io/biocontainers/seqtk:1.4--he4a0461_1'
+        docker = 'biocontainers/seqtk:1.4--he4a0461_1'
         report_tag = "SeqtkBaseCount"
     }
 
     locidex {
         // awaiting singluarity image build
         //singularity = "https://depot.galaxyproject.org/singularity/locidex%3A0.1.1--pyhdfd78af_1"
-        singularity = "quay.io/biocontainers/locidex:0.1.1--pyhdfd78af_1"
-        docker = "quay.io/biocontainers/locidex:0.1.1--pyhdfd78af_1"
+        singularity = "biocontainers/locidex:0.1.1--pyhdfd78af_1"
+        docker = "biocontainers/locidex:0.1.1--pyhdfd78af_1"
         min_evalue = params.lx_min_evalue
         min_dna_len = params.lx_min_dna_len
         min_aa_len = params.lx_min_aa_len
@@ -249,7 +249,7 @@ params {
     fastp {
         fastq_ext = ".trimmed.fastq.gz"
         singularity = 'https://depot.galaxyproject.org/singularity/fastp%3A0.23.2--hb7a2d85_2'
-        docker = 'quay.io/biocontainers/fastp:0.23.2--hb7a2d85_2'
+        docker = 'biocontainers/fastp:0.23.2--hb7a2d85_2'
         html_ext = ".html"
         json_ext = ".json"
         report_tag = "FastP"
@@ -296,7 +296,7 @@ params {
             hq = "--pacbio-hifi" // TODO all reads are marked as hifi
         }
         singularity = 'https://depot.galaxyproject.org/singularity/flye:2.9--py39h6935b12_1'
-        docker = 'quay.io/biocontainers/flye:2.9.2--py39h6935b12_0'
+        docker = 'biocontainers/flye:2.9.2--py39h6935b12_0'
         fasta_ext = ".fasta.gz"
         gfa_ext = ".gfa.gz"
         gv_ext = ".gv.gz"
@@ -310,7 +310,7 @@ params {
     // SPADES options
     spades {
         singularity = 'https://depot.galaxyproject.org/singularity/spades:3.15.5--h95f258a_1'
-        docker = 'quay.io/biocontainers/spades:3.15.5--h95f258a_1'
+        docker = 'biocontainers/spades:3.15.5--h95f258a_1'
         outdir = "assembly"
         scaffolds_ext = ".scaffolds.fasta.gz"
         contigs_ext = ".contigs.fasta.gz"
@@ -329,7 +329,7 @@ params {
     // TODO add to docs
     seqkit {
         singularity = 'https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0'
-        docker = 'quay.io/biocontainers/seqkit:2.2.0--h9ee0642_0'
+        docker = 'biocontainers/seqkit:2.2.0--h9ee0642_0'
         report_ext = ".tsv"
         fasta_ext = ".filtered.fasta.gz"
         filter_field = "max_len"
@@ -341,7 +341,7 @@ params {
     // QUAST args
     quast{
         singularity = 'https://depot.galaxyproject.org/singularity/quast%3A5.2.0--py39pl5321h4e691d4_3' // not all Quast containers work, might get file system error with BWA, if issue persists reads can be not passed to the module instead
-        docker = 'quay.io/biocontainers/quast:5.2.0--py39pl5321h4e691d4_3'
+        docker = 'biocontainers/quast:5.2.0--py39pl5321h4e691d4_3'
         suffix = "quast"
         report_base = "report"
         report_prefix = "transposed_"
@@ -359,7 +359,7 @@ params {
     checkm {
         // TODO add to trouble shooting if checkm fails and provides EOF errors, to try changing the container
         singularity = 'https://depot.galaxyproject.org/singularity/checkm-genome%3A1.2.2--pyhdfd78af_1'
-        docker = 'quay.io/biocontainers/checkm-genome:1.2.2--pyhdfd78af_1'
+        docker = 'biocontainers/checkm-genome:1.2.2--pyhdfd78af_1'
         alignment_ext = ".genes.aln"
         results_ext = ".results.txt"
         tsv_ext = ".tsv"
@@ -373,7 +373,7 @@ params {
     // Kraken args
     kraken {
         singularity = 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0'
-        docker = 'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0'
+        docker = 'biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0'
         db = params.kraken2_db
         classified_suffix = "classified"
         unclassified_suffix = "unclassified"
@@ -390,7 +390,7 @@ params {
 
     mlst {
         singularity = "https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1"
-        docker = "quay.io/biocontainers/mlst:2.19.0--hdfd78af_1"
+        docker = "biocontainers/mlst:2.19.0--hdfd78af_1"
         args = ""
         tsv_ext = ".tsv"
         json_ext = ".json"
@@ -399,7 +399,7 @@ params {
 
     mash {
         singularity = "https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1"
-        docker = 'quay.io/biocontainers/mash:2.3--he348c14_1'
+        docker = 'biocontainers/mash:2.3--he348c14_1'
         // going forward labeled with _ext include '.'
         mash_ext = ".screen" //TODO refactor out of utility workflow
         output_reads_ext = ".reads.screen"
@@ -431,7 +431,7 @@ params {
     r_contaminants {
         // container contains minimap2 and samtools
         singularity = "https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3161f532a5ea6f1dec9be5667c9efc2afdac6104-0"
-        docker = "quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3161f532a5ea6f1dec9be5667c9efc2afdac6104-0"
+        docker = "biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3161f532a5ea6f1dec9be5667c9efc2afdac6104-0"
         phix_fa = ""
         homo_sapiens_fa = ""
         pacbio_mg = ""
@@ -468,7 +468,7 @@ params {
 
     racon {
         singularity = 'https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1'
-        docker = 'quay.io/biocontainers/racon:1.4.20--h9a82719_1'
+        docker = 'biocontainers/racon:1.4.20--h9a82719_1'
         consensus_suffix = "_assembly_consensus.fasta"
         consensus_ext = ".fasta.gz"
         outdir = "polished"
@@ -476,7 +476,7 @@ params {
 
     pilon {
         singularity = 'https://depot.galaxyproject.org/singularity/pilon%3A1.24--hdfd78af_0'
-        docker = 'quay.io/biocontainers/pilon:1.24--hdfd78af_0'
+        docker = 'biocontainers/pilon:1.24--hdfd78af_0'
         outdir = "pilon"
         fasta_ext = ".fasta.gz"
         fasta_outdir = "fasta"
@@ -507,7 +507,7 @@ params {
 
     medaka {
         singularity = 'https://depot.galaxyproject.org/singularity/medaka%3A1.8.0--py38hdaa7744_0'
-        docker = 'quay.io/biocontainers/medaka:1.8.0--py38hdaa7744_0'
+        docker = 'biocontainers/medaka:1.8.0--py38hdaa7744_0'
         model = params.nanopore_chemistry
         fasta_ext = ".fa.gz"
         outdir = "medaka"
@@ -516,7 +516,7 @@ params {
 
     unicycler {
         singularity = 'https://depot.galaxyproject.org/singularity/unicycler%3A0.5.0--py38h3b68952_2'
-        docker = 'quay.io/biocontainers/unicycler:0.5.0--py38h3b68952_2'
+        docker = 'biocontainers/unicycler:0.5.0--py38h3b68952_2'
         scaffolds_ext = ".scaffolds.fa.gz"
         assembly_ext = ".assembly.gfa.gz"
         log_ext = ".unicycler.log"
@@ -527,7 +527,7 @@ params {
 
     mobsuite_recon {
         singularity = 'https://depot.galaxyproject.org/singularity/mob_suite%3A3.0.3--pyhdfd78af_0'
-        docker = 'quay.io/biocontainers/mob_suite:3.0.3--pyhdfd78af_0'
+        docker = 'biocontainers/mob_suite:3.0.3--pyhdfd78af_0'
         args = { "" }
         fasta_ext = ".fasta"
         results_ext = ".txt"
@@ -538,8 +538,8 @@ params {
     }
 
     staramr {
-        singularity = "quay.io/biocontainers/staramr:0.10.0--pyhdfd78af_0"
-        docker = "quay.io/biocontainers/staramr:0.10.0--pyhdfd78af_0"
+        singularity = "biocontainers/staramr:0.10.0--pyhdfd78af_0"
+        docker = "biocontainers/staramr:0.10.0--pyhdfd78af_0"
         point_finder_db_default = null
         db = null
         tsv_ext = ".tsv"
@@ -560,7 +560,7 @@ params {
     bakta {
         // TODO verify bakta version in scripts so that greater than 1.8 exists for force options
         singularity = 'https://depot.galaxyproject.org/singularity/bakta%3A1.8.1--pyhdfd78af_0'
-        docker = 'quay.io/biocontainers/bakta:1.8.1--pyhdfd78af_0'
+        docker = 'biocontainers/bakta:1.8.1--pyhdfd78af_0'
         db = params.bakta_db
         output_dir = "bakta"
         embl_ext = ".embl"
@@ -580,7 +580,7 @@ params {
 
     bandage {
         singularity = 'https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2'
-        docker = 'quay.io/biocontainers/bandage:0.8.1--hc9558a2_2'
+        docker = 'biocontainers/bandage:0.8.1--hc9558a2_2'
         svg_ext = ".svg"
         outdir = "bandage"
 
@@ -592,7 +592,7 @@ params {
 
     ectyper {
         singularity = 'https://depot.galaxyproject.org/singularity/ectyper:1.0.0--pyhdfd78af_1'
-        docker = 'quay.io/biocontainers/ectyper:1.0.0--pyhdfd78af_1'
+        docker = 'biocontainers/ectyper:1.0.0--pyhdfd78af_1'
         log_ext = ".log"
         tsv_ext = ".tsv"
         txt_ext = ".txt"
@@ -608,7 +608,7 @@ params {
 
     kleborate {
         singularity = 'https://depot.galaxyproject.org/singularity/kleborate:2.1.0--pyhdfd78af_1'
-        docker = 'quay.io/biocontainers/kleborate:2.1.0--pyhdfd78af_1'
+        docker = 'biocontainers/kleborate:2.1.0--pyhdfd78af_1'
         txt_ext = ".results.txt"
         report_tag = "Kleborate${params.subtyping_report.report_tag}"
         header_p = true
@@ -617,7 +617,7 @@ params {
     spatyper {
         // TODO figure out what repeats input is
         singularity = 'https://depot.galaxyproject.org/singularity/spatyper:0.3.3--pyhdfd78af_3'
-        docker = 'quay.io/biocontainers/spatyper:0.3.3--pyhdfd78af_3'
+        docker = 'biocontainers/spatyper:0.3.3--pyhdfd78af_3'
         tsv_ext = ".tsv"
         report_tag = "SpaTyper${params.subtyping_report.report_tag}"
         header_p = true
@@ -627,7 +627,7 @@ params {
 
     sistr {
         singularity = "https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.1--pyh864c0ab_2"
-        docker = 'quay.io/biocontainers/sistr_cmd:1.1.1--pyh864c0ab_2'
+        docker = 'biocontainers/sistr_cmd:1.1.1--pyh864c0ab_2'
         tsv_ext = ".tab"
         allele_fasta_ext = ".allele.fasta"
         allele_json_ext = ".allele.json"
@@ -639,7 +639,7 @@ params {
 
     lissero {
         singularity = 'https://depot.galaxyproject.org/singularity/lissero:0.4.9--py_0'
-        docker = 'quay.io/biocontainers/lissero:0.4.9--py_0'
+        docker = 'biocontainers/lissero:0.4.9--py_0'
         tsv_ext = ".tsv"
         report_tag = "LISSERO${params.subtyping_report.report_tag}"
         header_p = true
@@ -648,7 +648,7 @@ params {
     shigeifinder {
         container_version = '1.3.2' // update version info with containers as it is not included in shigeifinder
         singularity = 'https://depot.galaxyproject.org/singularity/shigeifinder:1.3.2--pyhdfd78af_0'
-        docker = 'quay.io/biocontainers/shigeifinder:1.3.2--pyhdfd78af_0'
+        docker = 'biocontainers/shigeifinder:1.3.2--pyhdfd78af_0'
         tsv_ext = ".tsv"
         report_tag = "Shigeifinder${params.subtyping_report.report_tag}"
         header_p = true
@@ -656,7 +656,7 @@ params {
 
     //shigatyper {
     //    singularity = 'https://depot.galaxyproject.org/singularity/shigatyper%3A2.0.1--pyhdfd78af_0'
-    //    docker = 'quay.io/biocontainers/shigatyper:2.0.1--pyhdfd78af_0'
+    //    docker = 'biocontainers/shigatyper:2.0.1--pyhdfd78af_0'
     //    tsv_ext = ".tsv"
     //    report_tag = "ShigaTyper${params.subtyping_report.report_tag}"
     //    //report_tag = params.subtyping_report.report_tag
@@ -1019,6 +1019,14 @@ profiles {
     test { includeConfig 'conf/test.config' }
 }
 
+// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
+// Set to your registry if you have a mirror of containers
+apptainer.registry   = 'quay.io'
+docker.registry      = 'quay.io'
+podman.registry      = 'quay.io'
+singularity.registry = 'quay.io'
+
 plugins {
     //id 'nf-validation@2.0.0'
     id 'nf-validation@1.1.3'

From 5f7c88fbf68c841adccb889eb100fdff96b003ef Mon Sep 17 00:00:00 2001
From: Matthew Wells <mattwells9@shaw.ca>
Date: Thu, 11 Jul 2024 15:25:02 -0500
Subject: [PATCH 2/8] updated changelog

---
 CHANGELOG.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6a9378c4..58d6bfc3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,13 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Unreleased
+
+### `Changed`
+
+- Removed quay.io docker repo tags [PR 94](https://github.com/phac-nml/mikrokondo/pull/94)
+
+
 ## [0.3.0] - 2024-07-04
 
 ### `Changed`

From 86ca9aa4cdcae5911fd19bdfdd0411f96c2b9be0 Mon Sep 17 00:00:00 2001
From: Matthew Wells <mattwells9@shaw.ca>
Date: Thu, 11 Jul 2024 16:28:35 -0500
Subject: [PATCH 3/8] updated test snapshots

---
 .../local/qc_assemblies/qc_assemblies.nf.test.snap | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tests/subworkflows/local/qc_assemblies/qc_assemblies.nf.test.snap b/tests/subworkflows/local/qc_assemblies/qc_assemblies.nf.test.snap
index ba4f6864..72931e4c 100644
--- a/tests/subworkflows/local/qc_assemblies/qc_assemblies.nf.test.snap
+++ b/tests/subworkflows/local/qc_assemblies/qc_assemblies.nf.test.snap
@@ -27,7 +27,7 @@
                         },
                         {
                             "singularity": "https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0",
-                            "docker": "quay.io/biocontainers/seqkit:2.2.0--h9ee0642_0",
+                            "docker": "biocontainers/seqkit:2.2.0--h9ee0642_0",
                             "report_ext": ".tsv",
                             "fasta_ext": ".filtered.fasta.gz",
                             "filter_field": "max_len",
@@ -51,7 +51,7 @@
                         },
                         {
                             "singularity": "https://depot.galaxyproject.org/singularity/quast%3A5.2.0--py39pl5321h4e691d4_3",
-                            "docker": "quay.io/biocontainers/quast:5.2.0--py39pl5321h4e691d4_3",
+                            "docker": "biocontainers/quast:5.2.0--py39pl5321h4e691d4_3",
                             "suffix": "quast",
                             "report_base": "report",
                             "report_prefix": "transposed_",
@@ -72,7 +72,7 @@
                         },
                         {
                             "singularity": "https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0",
-                            "docker": "quay.io/biocontainers/seqkit:2.2.0--h9ee0642_0",
+                            "docker": "biocontainers/seqkit:2.2.0--h9ee0642_0",
                             "report_ext": ".tsv",
                             "fasta_ext": ".filtered.fasta.gz",
                             "filter_field": "max_len",
@@ -114,7 +114,7 @@
                         },
                         {
                             "singularity": "https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0",
-                            "docker": "quay.io/biocontainers/seqkit:2.2.0--h9ee0642_0",
+                            "docker": "biocontainers/seqkit:2.2.0--h9ee0642_0",
                             "report_ext": ".tsv",
                             "fasta_ext": ".filtered.fasta.gz",
                             "filter_field": "max_len",
@@ -138,7 +138,7 @@
                         },
                         {
                             "singularity": "https://depot.galaxyproject.org/singularity/quast%3A5.2.0--py39pl5321h4e691d4_3",
-                            "docker": "quay.io/biocontainers/quast:5.2.0--py39pl5321h4e691d4_3",
+                            "docker": "biocontainers/quast:5.2.0--py39pl5321h4e691d4_3",
                             "suffix": "quast",
                             "report_base": "report",
                             "report_prefix": "transposed_",
@@ -159,7 +159,7 @@
                         },
                         {
                             "singularity": "https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0",
-                            "docker": "quay.io/biocontainers/seqkit:2.2.0--h9ee0642_0",
+                            "docker": "biocontainers/seqkit:2.2.0--h9ee0642_0",
                             "report_ext": ".tsv",
                             "fasta_ext": ".filtered.fasta.gz",
                             "filter_field": "max_len",
@@ -182,6 +182,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.0"
         },
-        "timestamp": "2024-06-20T12:08:01.726320878"
+        "timestamp": "2024-07-11T16:26:45.559362978"
     }
 }
\ No newline at end of file

From b0905219ec669b50ac37d83bf9030874864759b1 Mon Sep 17 00:00:00 2001
From: Steven Sutcliffe <sgsutcliffe@gmail.com>
Date: Fri, 30 Aug 2024 11:33:05 -0400
Subject: [PATCH 4/8] Added container override process for docker hub container

---
 modules/local/pilon_polisher.nf |  2 +-
 nextflow.config                 | 10 +++-------
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/modules/local/pilon_polisher.nf b/modules/local/pilon_polisher.nf
index ed50969c..16f01e07 100644
--- a/modules/local/pilon_polisher.nf
+++ b/modules/local/pilon_polisher.nf
@@ -4,7 +4,7 @@ process PILON_ITER {
     tag "$meta.id"
     label 'process_medium'
     memory  {task.memory * task.attempt}
-    container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
+    container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.override_configured_container_registry != false ? task.ext.parameters.get('docker') : task.ext.parameters.get('private_repository')}"
 
     input:
     tuple val(meta), path(reads), path(contigs)
diff --git a/nextflow.config b/nextflow.config
index b8d445ca..61bb5474 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -490,6 +490,7 @@ params {
     pilon_iterative {
         singularity = 'docker.io/mwells14/pilonpolisher:0.0.1' // Docker containers will be converted to singularity
         docker = 'docker.io/mwells14/pilonpolisher:0.0.1'
+        private_repository = 'mwells14/pilonpolisher:0.0.1'
         outdir = "pilon"
         fasta_ext = ".fasta.gz"
         fasta_outdir = "fasta"
@@ -1019,13 +1020,8 @@ profiles {
     test { includeConfig 'conf/test.config' }
 }
 
-// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
-// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
-// Set to your registry if you have a mirror of containers
-apptainer.registry   = 'quay.io'
-docker.registry      = 'quay.io'
-podman.registry      = 'quay.io'
-singularity.registry = 'quay.io'
+// Override the default Docker registry when required
+process.ext.override_configured_container_registry = true
 
 plugins {
     //id 'nf-validation@2.0.0'

From 697cbb2b5a97750cdf7bb49e43b7913aacc2b020 Mon Sep 17 00:00:00 2001
From: Steven Sutcliffe <sgsutcliffe@gmail.com>
Date: Fri, 30 Aug 2024 12:31:45 -0400
Subject: [PATCH 5/8] Added default registry as quay.io

---
 nextflow.config | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 61bb5474..937b0f49 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1020,8 +1020,16 @@ profiles {
     test { includeConfig 'conf/test.config' }
 }
 
+// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
+// Set to your registry if you have a mirror of containers
+apptainer.registry   = 'quay.io'
+docker.registry      = 'quay.io'
+podman.registry      = 'quay.io'
+singularity.registry = 'quay.io'
+
 // Override the default Docker registry when required
-process.ext.override_configured_container_registry = true
+process.ext.override_configured_container_registry = false
 
 plugins {
     //id 'nf-validation@2.0.0'

From 4f11807eaaa3ebc1070831cec9a4c896e559e7d9 Mon Sep 17 00:00:00 2001
From: Steven Sutcliffe <sgsutcliffe@gmail.com>
Date: Fri, 30 Aug 2024 13:00:56 -0400
Subject: [PATCH 6/8] Updated params.locidex, and modules that use it, to have
 override default container option

---
 modules/local/locidex_extract.nf | 2 +-
 modules/local/locidex_report.nf  | 2 +-
 modules/local/locidex_search.nf  | 2 +-
 nextflow.config                  | 1 +
 4 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/modules/local/locidex_extract.nf b/modules/local/locidex_extract.nf
index 0b513838..ff2220cc 100644
--- a/modules/local/locidex_extract.nf
+++ b/modules/local/locidex_extract.nf
@@ -7,7 +7,7 @@ process LOCIDEX_EXTRACT {
 
     tag "$meta.id"
     label "process_low"
-    container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
+    container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.override_configured_container_registry != false ? task.ext.parameters.get('docker') : task.ext.parameters.get('private_repository')}"
 
 
     input:
diff --git a/modules/local/locidex_report.nf b/modules/local/locidex_report.nf
index f1a4db7e..dcd34656 100644
--- a/modules/local/locidex_report.nf
+++ b/modules/local/locidex_report.nf
@@ -5,7 +5,7 @@
 process LOCIDEX_REPORT {
     tag "$meta.id"
     label "process_low"
-    container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
+    container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.override_configured_container_registry != false ? task.ext.parameters.get('docker') : task.ext.parameters.get('private_repository')}"
 
     input:
     tuple val(meta), path(seq_store)
diff --git a/modules/local/locidex_search.nf b/modules/local/locidex_search.nf
index 6123e4cd..d2c60121 100644
--- a/modules/local/locidex_search.nf
+++ b/modules/local/locidex_search.nf
@@ -6,7 +6,7 @@ process LOCIDEX_SEARCH {
 
     tag "$meta.id"
     label "process_medium"
-    container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.parameters.get('docker')}"
+    container "${workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? task.ext.parameters.get('singularity') : task.ext.override_configured_container_registry != false ? task.ext.parameters.get('docker') : task.ext.parameters.get('private_repository')}"
 
     input:
     tuple val(meta), path(fasta), path(db)
diff --git a/nextflow.config b/nextflow.config
index 586d0051..4d6c755d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -216,6 +216,7 @@ params {
         // awaiting singluarity image build
         singularity = "docker.io/mwells14/locidex:0.2.3"
         docker = "docker.io/mwells14/locidex:0.2.3"
+        private_repository = 'mwells14/locidex:0.2.3'
         min_evalue = params.lx_min_evalue
         min_dna_len = params.lx_min_dna_len
         min_aa_len = params.lx_min_aa_len

From 0be594bc0ac78fdc0bc95870c5fdaecf2ae4faf3 Mon Sep 17 00:00:00 2001
From: Steven Sutcliffe <sgsutcliffe@gmail.com>
Date: Fri, 30 Aug 2024 14:09:25 -0400
Subject: [PATCH 7/8] Set process.ext.override.. to true by default

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 4d6c755d..7496b7fc 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1052,7 +1052,7 @@ podman.registry      = 'quay.io'
 singularity.registry = 'quay.io'
 
 // Override the default Docker registry when required
-process.ext.override_configured_container_registry = false
+process.ext.override_configured_container_registry = true
 
 plugins {
     //id 'nf-validation@2.0.0'

From 0419a5afa2dea7b002cf6c3fc2f2cd9be78adaf6 Mon Sep 17 00:00:00 2001
From: Steven Sutcliffe <sgsutcliffe@gmail.com>
Date: Fri, 30 Aug 2024 16:17:12 -0400
Subject: [PATCH 8/8] Updated Python container to quay.io/biocontainer

---
 nextflow.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 7496b7fc..9475b78c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -193,8 +193,8 @@ params {
 
     // Python container, May switch for pypy3
     python3 {
-        singularity = "biocontainers/staramr:0.10.0--pyhdfd78af_0"
-        docker = "biocontainers/staramr:0.10.0--pyhdfd78af_0"
+        singularity = "https://depot.galaxyproject.org/singularity/python:3.12"
+        docker = "biocontainers/python:3.12"
     }
 
     seqtk {