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dropped quay.io from docker paths #94

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merged 10 commits into from
Aug 30, 2024
Merged

dropped quay.io from docker paths #94

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20b71fa
dropped quay.io from docker paths
mattheww95 Jul 11, 2024
5f7c88f
updated changelog
mattheww95 Jul 11, 2024
86ca9aa
updated test snapshots
mattheww95 Jul 11, 2024
98a43d3
Merge branch 'dev' into patch/registries
mattheww95 Jul 25, 2024
b090521
Added container override process for docker hub container
sgsutcliffe Aug 30, 2024
697cbb2
Added default registry as quay.io
sgsutcliffe Aug 30, 2024
e09cf9f
Merge branch 'dev' into patch/registries
sgsutcliffe Aug 30, 2024
4f11807
Updated params.locidex, and modules that use it, to have override def…
sgsutcliffe Aug 30, 2024
0be594b
Set process.ext.override.. to true by default
sgsutcliffe Aug 30, 2024
0419a5a
Updated Python container to quay.io/biocontainer
sgsutcliffe Aug 30, 2024
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76 changes: 42 additions & 34 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
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args = { "" }
report_tag = "Abricate"
header_p = true
Expand All @@ -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"
Expand All @@ -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
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand All @@ -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"
Expand All @@ -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"
Expand All @@ -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_"
Expand All @@ -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"
Expand All @@ -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"
Expand All @@ -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"
Expand All @@ -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"
Expand Down Expand Up @@ -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 = ""
Expand Down Expand Up @@ -468,15 +468,15 @@ 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"
}

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"
Expand Down Expand Up @@ -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"
Expand All @@ -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"
Expand All @@ -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"
Expand All @@ -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"
Expand All @@ -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"
Expand All @@ -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"

Expand All @@ -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"
Expand All @@ -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${params.subtyping_report.report_tag}"
header_p = true
Expand All @@ -617,7 +617,7 @@ params {
spatyper {
// TODO figure out what repeats input is
singularity = 'https://depot.galaxyproject.org/singularity/spatyper:0.3.3--pyhdfd78af_3'
docker = 'quay.io/biocontainers/spatyper:0.3.3--pyhdfd78af_3'
docker = 'biocontainers/spatyper:0.3.3--pyhdfd78af_3'
tsv_ext = ".tsv"
report_tag = "SpaTyper${params.subtyping_report.report_tag}"
header_p = true
Expand All @@ -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"
Expand All @@ -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${params.subtyping_report.report_tag}"
header_p = true
Expand All @@ -648,15 +648,15 @@ params {
shigeifinder {
container_version = '1.3.2' // update version info with containers as it is not included in shigeifinder
singularity = 'https://depot.galaxyproject.org/singularity/shigeifinder:1.3.2--pyhdfd78af_0'
docker = 'quay.io/biocontainers/shigeifinder:1.3.2--pyhdfd78af_0'
docker = 'biocontainers/shigeifinder:1.3.2--pyhdfd78af_0'
tsv_ext = ".tsv"
report_tag = "Shigeifinder${params.subtyping_report.report_tag}"
header_p = true
}

//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
Expand Down Expand Up @@ -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 '[email protected]'
id '[email protected]'
Expand Down
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