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🎨🐳 Replace jason-c-kwan with jasonkwan for docker images #217

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merged 1 commit into from
Jan 12, 2022
Merged

🎨🐳 Replace jason-c-kwan with jasonkwan for docker images #217

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8 changes: 4 additions & 4 deletions Makefile
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Expand Up @@ -63,14 +63,14 @@ install: setup.py
test_environment: tests/requirements.txt
python3 -m pip install --requirement=tests/requirements.txt

## Build docker image from Dockerfile (auto-taggged as jason-c-kwan/autometa:<current-branch>)
## Build docker image from Dockerfile (auto-taggged as jasonkwan/autometa:<current-branch>)
image: Dockerfile
docker build . -t jason-c-kwan/autometa:`git branch --show-current`
docker build . -t jasonkwan/autometa:`git branch --show-current`

## Build necessary docker images for nextflow modules from Dockerfiles in docker/modules
modules-images: docker/modules/get_genomes_for_mock.Dockerfile docker/modules/mock_data_reporter.Dockerfile
docker build docker/modules/ -t jason-c-kwan/autometa-nf-modules-get_genomes_for_mock -f docker/modules/get_genomes_for_mock.Dockerfile
docker build docker/modules/ -t jason-c-kwan/autometa-nf-modules-mock_data_reporter -f docker/modules/mock_data_reporter.Dockerfile
docker build docker/modules/ -t jasonkwan/autometa-nf-modules-get_genomes_for_mock -f docker/modules/get_genomes_for_mock.Dockerfile
docker build docker/modules/ -t jasonkwan/autometa-nf-modules-mock_data_reporter -f docker/modules/mock_data_reporter.Dockerfile

## Build documentation for autometa.readthedocs.io
docs:
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2 changes: 1 addition & 1 deletion modules/local/analyze_kmers.nf
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Expand Up @@ -15,7 +15,7 @@ process ANALYZE_KMERS {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/autometa"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

input:
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2 changes: 1 addition & 1 deletion modules/local/bin_contigs.nf
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Expand Up @@ -15,7 +15,7 @@ process BIN_CONTIGS {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

input:
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2 changes: 1 addition & 1 deletion modules/local/binning_summary.nf
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Expand Up @@ -17,7 +17,7 @@ process BINNING_SUMMARY {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

input:
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2 changes: 1 addition & 1 deletion modules/local/get_genomes_for_mock.nf
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Expand Up @@ -8,7 +8,7 @@ process GET_GENOMES_FOR_MOCK {
def genome_count = options.args2.tokenize('|').size()
tag "fetching ${genome_count} genomes"
conda (params.enable_conda ? "bioconda::emboss=6.6.0" : null)
container "jason-c-kwan/autometa-nf-modules-get_genomes_for_mock"
container "jasonkwan/autometa-nf-modules-get_genomes_for_mock"

output:
path "metagenome.fna.gz", emit: metagenome
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2 changes: 1 addition & 1 deletion modules/local/hmmer_hmmsearch_filter.nf
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Expand Up @@ -29,7 +29,7 @@ process HMMER_HMMSEARCH_FILTER {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

input:
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2 changes: 1 addition & 1 deletion modules/local/length_table.nf
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Expand Up @@ -15,7 +15,7 @@ process LENGTH_TABLE {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

input:
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2 changes: 1 addition & 1 deletion modules/local/majority_vote.nf
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Expand Up @@ -17,7 +17,7 @@ process MAJORITY_VOTE {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

input:
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2 changes: 1 addition & 1 deletion modules/local/markers.nf
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Expand Up @@ -13,7 +13,7 @@ process MARKERS {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

input:
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2 changes: 1 addition & 1 deletion modules/local/merge_tsv.nf
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Expand Up @@ -16,7 +16,7 @@ process MERGE_TSV_WITH_HEADERS {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

input:
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2 changes: 1 addition & 1 deletion modules/local/mock_data_reporter.nf
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Expand Up @@ -12,7 +12,7 @@ process MOCK_DATA_REPORT {
publishDir "${params.outdir_internal}/${options.publish_dir}",
mode: params.publish_dir_mode

container "jason-c-kwan/autometa-nf-modules-mock_data_reporter"
container "jasonkwan/autometa-nf-modules-mock_data_reporter"


input:
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2 changes: 1 addition & 1 deletion modules/local/parse_bed.nf
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Expand Up @@ -15,7 +15,7 @@ process PARSE_BED {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

input:
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2 changes: 1 addition & 1 deletion modules/local/prepare_lca.nf
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Expand Up @@ -15,7 +15,7 @@ process PREPARE_LCA {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

storeDir 'db/lca'
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2 changes: 1 addition & 1 deletion modules/local/reduce_lca.nf
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Expand Up @@ -15,7 +15,7 @@ process REDUCE_LCA {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

input:
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2 changes: 1 addition & 1 deletion modules/local/spades_kmer_coverage.nf
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Expand Up @@ -16,7 +16,7 @@ process SPADES_KMER_COVERAGE {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

input:
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2 changes: 1 addition & 1 deletion modules/local/split_kingdoms.nf
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Expand Up @@ -16,7 +16,7 @@ process SPLIT_KINGDOMS {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

input:
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2 changes: 1 addition & 1 deletion modules/local/unclustered_recruitment.nf
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Expand Up @@ -16,7 +16,7 @@ process RECRUIT {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

input:
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6 changes: 3 additions & 3 deletions subworkflows/local/prepare_ncbi_taxinfo.nf
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Expand Up @@ -17,7 +17,7 @@ process TEST_DOWNLOAD {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

output:
Expand All @@ -40,7 +40,7 @@ process DOWNLOAD_ACESSION2TAXID {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

output:
Expand Down Expand Up @@ -73,7 +73,7 @@ process DOWNLOAD_TAXDUMP {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

output:
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4 changes: 2 additions & 2 deletions subworkflows/local/prepare_nr.nf
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Expand Up @@ -18,7 +18,7 @@ process DOWNLOAD_NR {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

output:
Expand Down Expand Up @@ -48,7 +48,7 @@ process TEST_DOWNLOAD {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
} else {
container "jason-c-kwan/autometa:${params.autometa_image_tag}"
container "jasonkwan/autometa:${params.autometa_image_tag}"
}

output:
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