mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 01:36:04 +00:00
Remove samtools/bam2fq module
This commit is contained in:
sofstam
parent
8745fc625c
commit
021f5f0a22
3 changed files with 127 additions and 159 deletions
173
modules.json
173
modules.json
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@ -8,219 +8,298 @@
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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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"modules"
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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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"modules"
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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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"modules"
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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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"installed_by": [
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"modules"
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]
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},
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},
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"krakentools/kreport2krona": {
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"krakentools/kreport2krona": {
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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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"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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"installed_by": [
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"modules"
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]
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},
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},
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"krona/ktimporttaxonomy": {
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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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"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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"krona/ktimporttext": {
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"krona/ktimporttext": {
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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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"malt/run": {
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"malt/run": {
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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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"megan/rma2info": {
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"megan/rma2info": {
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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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"metaphlan3/mergemetaphlantables": {
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"metaphlan3/mergemetaphlantables": {
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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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"metaphlan3/metaphlan3": {
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"metaphlan3/metaphlan3": {
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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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"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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"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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"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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"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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"motus/merge": {
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"motus/merge": {
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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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"motus/profile": {
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"motus/profile": {
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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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"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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"installed_by": [
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"modules"
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]
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},
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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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"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/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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"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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"modules"
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"samtools/bam2fq": {
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]
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"branch": "master",
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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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"samtools/fastq": {
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"samtools/fastq": {
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"branch": "master",
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"branch": "master",
|
||||||
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
|
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"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": "ffa9641ee18f88aff974257cb50ba3cf8f7d143c",
|
"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"
|
||||||
|
]
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
56
modules/nf-core/samtools/bam2fq/main.nf
generated
56
modules/nf-core/samtools/bam2fq/main.nf
generated
|
|
@ -1,56 +0,0 @@
|
||||||
process SAMTOOLS_BAM2FQ {
|
|
||||||
tag "$meta.id"
|
|
||||||
label 'process_low'
|
|
||||||
|
|
||||||
conda "bioconda::samtools=1.16.1"
|
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
||||||
'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
|
|
||||||
'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
|
|
||||||
|
|
||||||
input:
|
|
||||||
tuple val(meta), path(inputbam)
|
|
||||||
val split
|
|
||||||
|
|
||||||
output:
|
|
||||||
tuple val(meta), path("*.fq.gz"), emit: reads
|
|
||||||
path "versions.yml" , emit: versions
|
|
||||||
|
|
||||||
when:
|
|
||||||
task.ext.when == null || task.ext.when
|
|
||||||
|
|
||||||
script:
|
|
||||||
def args = task.ext.args ?: ''
|
|
||||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
||||||
|
|
||||||
if (split){
|
|
||||||
"""
|
|
||||||
samtools \\
|
|
||||||
bam2fq \\
|
|
||||||
$args \\
|
|
||||||
-@ $task.cpus \\
|
|
||||||
-1 ${prefix}_1.fq.gz \\
|
|
||||||
-2 ${prefix}_2.fq.gz \\
|
|
||||||
-0 ${prefix}_other.fq.gz \\
|
|
||||||
-s ${prefix}_singleton.fq.gz \\
|
|
||||||
$inputbam
|
|
||||||
|
|
||||||
cat <<-END_VERSIONS > versions.yml
|
|
||||||
"${task.process}":
|
|
||||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
|
||||||
END_VERSIONS
|
|
||||||
"""
|
|
||||||
} else {
|
|
||||||
"""
|
|
||||||
samtools \\
|
|
||||||
bam2fq \\
|
|
||||||
$args \\
|
|
||||||
-@ $task.cpus \\
|
|
||||||
$inputbam | gzip --no-name > ${prefix}_interleaved.fq.gz
|
|
||||||
|
|
||||||
cat <<-END_VERSIONS > versions.yml
|
|
||||||
"${task.process}":
|
|
||||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
|
||||||
END_VERSIONS
|
|
||||||
"""
|
|
||||||
}
|
|
||||||
}
|
|
||||||
55
modules/nf-core/samtools/bam2fq/meta.yml
generated
55
modules/nf-core/samtools/bam2fq/meta.yml
generated
|
|
@ -1,55 +0,0 @@
|
||||||
name: samtools_bam2fq
|
|
||||||
description: |
|
|
||||||
The module uses bam2fq method from samtools to
|
|
||||||
convert a SAM, BAM or CRAM file to FASTQ format
|
|
||||||
keywords:
|
|
||||||
- bam2fq
|
|
||||||
- samtools
|
|
||||||
- fastq
|
|
||||||
tools:
|
|
||||||
- samtools:
|
|
||||||
description: Tools for dealing with SAM, BAM and CRAM files
|
|
||||||
homepage: None
|
|
||||||
documentation: http://www.htslib.org/doc/1.1/samtools.html
|
|
||||||
tool_dev_url: None
|
|
||||||
doi: ""
|
|
||||||
licence: ["MIT"]
|
|
||||||
|
|
||||||
input:
|
|
||||||
- meta:
|
|
||||||
type: map
|
|
||||||
description: |
|
|
||||||
Groovy Map containing sample information
|
|
||||||
e.g. [ id:'test', single_end:false ]
|
|
||||||
- inputbam:
|
|
||||||
type: file
|
|
||||||
description: BAM/CRAM/SAM file
|
|
||||||
pattern: "*.{bam,cram,sam}"
|
|
||||||
- split:
|
|
||||||
type: boolean
|
|
||||||
description: |
|
|
||||||
TRUE/FALSE value to indicate if reads should be separated into
|
|
||||||
/1, /2 and if present other, or singleton.
|
|
||||||
Note: choosing TRUE will generate 4 different files.
|
|
||||||
Choosing FALSE will produce a single file, which will be interleaved in case
|
|
||||||
the input contains paired reads.
|
|
||||||
|
|
||||||
output:
|
|
||||||
- meta:
|
|
||||||
type: map
|
|
||||||
description: |
|
|
||||||
Groovy Map containing sample information
|
|
||||||
e.g. [ id:'test', single_end:false ]
|
|
||||||
- versions:
|
|
||||||
type: file
|
|
||||||
description: File containing software versions
|
|
||||||
pattern: "versions.yml"
|
|
||||||
- reads:
|
|
||||||
type: file
|
|
||||||
description: |
|
|
||||||
FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)
|
|
||||||
or a single interleaved .fq.gz file if the user chooses not to split the reads.
|
|
||||||
pattern: "*.fq.gz"
|
|
||||||
|
|
||||||
authors:
|
|
||||||
- "@lescai"
|
|
||||||
Loading…
Reference in a new issue