mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-25 02:59:55 +00:00
Fix linting
This commit is contained in:
James Fellows Yates
parent
1ccd0a0767
commit
da3d2d96e6
2 changed files with 79 additions and 40 deletions
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@ -54,7 +54,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
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## Quick Start
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## Quick Start
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1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`).
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1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`).
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2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
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2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
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117
modules.json
117
modules.json
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@ -7,35 +7,43 @@
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"nf-core": {
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"nf-core": {
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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": "ce7cf27e377fdacf7ebe8e75903ec70405ea1659"
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"git_sha": "ce7cf27e377fdacf7ebe8e75903ec70405ea1659",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1"
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"git_sha": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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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@ -44,23 +52,28 @@
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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},
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},
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"eido/convert": {
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"eido/convert": {
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"branch": "master",
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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},
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},
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"eido/validate": {
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"eido/validate": {
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"branch": "master",
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "fc959214036403ad83efe7a41d43d0606c445cda"
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"git_sha": "fc959214036403ad83efe7a41d43d0606c445cda",
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"installed_by": ["modules"]
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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": "1e49f31e93c56a3832833eef90a02d3cde5a3f7e"
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"git_sha": "1e49f31e93c56a3832833eef90a02d3cde5a3f7e",
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"installed_by": ["modules"]
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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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@ -69,79 +82,98 @@
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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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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"krakentools/kreport2krona": {
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"branch": "master",
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "05649975c6611c6e007537a7984e186e12ae03af"
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"git_sha": "05649975c6611c6e007537a7984e186e12ae03af",
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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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"krona/ktimporttaxonomy": {
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"branch": "master",
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "6d9712f03ec2de8264a50ee4541a617e1e063b51"
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"git_sha": "6d9712f03ec2de8264a50ee4541a617e1e063b51",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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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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@ -150,31 +182,38 @@
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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": "2a4e85eb81875a572bb58133e37f84ba3cc484d7"
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"git_sha": "2a4e85eb81875a572bb58133e37f84ba3cc484d7",
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"installed_by": ["modules"]
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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},
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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": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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},
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},
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"samtools/index": {
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"samtools/index": {
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"branch": "master",
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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},
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},
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"samtools/stats": {
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"samtools/stats": {
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"branch": "master",
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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},
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},
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"samtools/view": {
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"samtools/view": {
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"branch": "master",
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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},
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},
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"untar": {
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"untar": {
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"branch": "master",
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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}
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}
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}
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}
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}
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}
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