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Updata taxpasta
This commit is contained in:
sofstam
parent
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commit
213f4e4f23
3 changed files with 132 additions and 48 deletions
172
modules.json
172
modules.json
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@ -8,217 +8,301 @@
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"adapterremoval": {
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"adapterremoval": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"bbmap/bbduk": {
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"bbmap/bbduk": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"bowtie2/align": {
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"bowtie2/align": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"bowtie2/build": {
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"bowtie2/build": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"bracken/bracken": {
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"bracken/bracken": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"bracken/combinebrackenoutputs": {
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"bracken/combinebrackenoutputs": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"cat/fastq": {
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"cat/fastq": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"centrifuge/centrifuge": {
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"centrifuge/centrifuge": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"centrifuge/kreport": {
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"centrifuge/kreport": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"custom/dumpsoftwareversions": {
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"custom/dumpsoftwareversions": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"diamond/blastx": {
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"diamond/blastx": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"falco": {
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"falco": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"],
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"installed_by": [
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"modules"
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],
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"patch": "modules/nf-core/falco/falco.diff"
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"patch": "modules/nf-core/falco/falco.diff"
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},
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},
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"fastp": {
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"fastp": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"fastqc": {
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"fastqc": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"filtlong": {
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"filtlong": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"gunzip": {
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"gunzip": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"kaiju/kaiju": {
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"kaiju/kaiju": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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},
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"kaiju/kaiju2krona": {
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"kaiju/kaiju2krona": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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]
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},
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},
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"kaiju/kaiju2table": {
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"kaiju/kaiju2table": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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]
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},
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},
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"kraken2/kraken2": {
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"kraken2/kraken2": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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]
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},
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},
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"krakentools/combinekreports": {
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"krakentools/combinekreports": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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},
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"krakentools/kreport2krona": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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},
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},
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"krakenuniq/preloadedkrakenuniq": {
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"krakenuniq/preloadedkrakenuniq": {
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"branch": "master",
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"branch": "master",
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"git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee",
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"git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee",
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"installed_by": ["modules"]
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},
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},
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"krona/ktimporttaxonomy": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"krona/ktimporttext": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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},
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"malt/run": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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},
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"megan/rma2info": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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},
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"metaphlan3/mergemetaphlantables": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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},
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},
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"metaphlan3/metaphlan3": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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},
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},
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"minimap2/align": {
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"minimap2/align": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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},
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},
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"minimap2/index": {
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"minimap2/index": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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},
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"motus/merge": {
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"motus/merge": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"motus/profile": {
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"motus/profile": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"multiqc": {
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"multiqc": {
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"branch": "master",
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"branch": "master",
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"git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
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"git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
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"installed_by": ["modules"]
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},
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"porechop/porechop": {
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"porechop/porechop": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
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"patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
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},
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},
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"prinseqplusplus": {
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"prinseqplusplus": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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},
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"samtools/bam2fq": {
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"samtools/bam2fq": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"samtools/index": {
|
"samtools/index": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"samtools/stats": {
|
"samtools/stats": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"samtools/view": {
|
"samtools/view": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"taxpasta/merge": {
|
"taxpasta/merge": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "fe58454add6225d2b7468e6d72a3a1f6a3149638",
|
"git_sha": "ffa9641ee18f88aff974257cb50ba3cf8f7d143c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"untar": {
|
"untar": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
6
modules/nf-core/taxpasta/merge/main.nf
generated
6
modules/nf-core/taxpasta/merge/main.nf
generated
|
|
@ -2,10 +2,10 @@ process TAXPASTA_MERGE {
|
||||||
tag "$meta.id"
|
tag "$meta.id"
|
||||||
label 'process_single'
|
label 'process_single'
|
||||||
|
|
||||||
conda "bioconda::taxpasta=0.2.0"
|
conda "bioconda::taxpasta=0.2.3"
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
'https://depot.galaxyproject.org/singularity/taxpasta:0.2.0--pyhdfd78af_0':
|
'https://depot.galaxyproject.org/singularity/taxpasta:0.2.3--pyhdfd78af_0':
|
||||||
'quay.io/biocontainers/taxpasta:0.2.0--pyhdfd78af_0' }"
|
'quay.io/biocontainers/taxpasta:0.2.3--pyhdfd78af_0' }"
|
||||||
|
|
||||||
|
|
||||||
input:
|
input:
|
||||||
|
|
|
||||||
2
modules/nf-core/taxpasta/merge/meta.yml
generated
2
modules/nf-core/taxpasta/merge/meta.yml
generated
|
|
@ -14,7 +14,7 @@ tools:
|
||||||
homepage: "https://taxpasta.readthedocs.io/"
|
homepage: "https://taxpasta.readthedocs.io/"
|
||||||
documentation: "https://taxpasta.readthedocs.io/"
|
documentation: "https://taxpasta.readthedocs.io/"
|
||||||
tool_dev_url: "https://github.com/taxprofiler/taxpasta"
|
tool_dev_url: "https://github.com/taxprofiler/taxpasta"
|
||||||
doi: ""
|
|
||||||
licence: "['Apache-2.0']"
|
licence: "['Apache-2.0']"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
|
|
|
||||||
Loading…
Reference in a new issue