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Merge pull request #117 from nf-core/dev
PR for 1.1.2 - Bugfix release
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.github/workflows/ci.yml

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- name: Download and tag image
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run: |
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docker pull nfcore/ampliseq:dev
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docker tag nfcore/ampliseq:dev nfcore/ampliseq:1.1.1
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docker tag nfcore/ampliseq:dev nfcore/ampliseq:1.1.2
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- name: Run test
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker

.travis.yml

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@@ -12,7 +12,7 @@ before_install:
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- '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && ([ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ] || [ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]))' # Pull the docker image first so the test doesn't wait for this
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- docker pull nfcore/ampliseq:dev
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# Fake the tag locally so that the pipeline runs properly
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- docker tag nfcore/ampliseq:dev nfcore/ampliseq:1.1.1
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- docker tag nfcore/ampliseq:dev nfcore/ampliseq:1.1.2
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install:
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# Install Nextflow

CHANGELOG.md

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# nf-core/ampliseq
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## nf-core/ampliseq version 1.1.2 - 2019
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* No further changes, except a bugfix for the [timezone](https://github.com/nf-core/ampliseq/issues/114) issue found by @marchoeppner
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* Specification of '--qiime_timezone' might be required to run the analysis appropriately
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## nf-core/ampliseq version 1.1.1 - 2019
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### Pipeline Updates
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* Update from QIIME2 v2018.6 to v2019.10, including DADA2 v1.6 to DADA2 v1.10
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* Export absolute abundance files into 'results/abundance-table/filtered/' for optional external secondary analysis
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### Bugfixes
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* [#78](https://github.com/nf-core/ampliseq/issues/78) - All sequenced classifed to the same species

Dockerfile

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@@ -2,7 +2,7 @@ FROM nfcore/base:1.7
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LABEL description="Docker image containing all requirements for nf-core/ampliseq pipeline"
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COPY environment.yml /
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RUN conda env create -f /environment.yml && conda clean -a
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ENV PATH /opt/conda/envs/nf-core-ampliseq-1.1.1/bin:$PATH
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ENV PATH /opt/conda/envs/nf-core-ampliseq-1.1.2/bin:$PATH
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## Required to build the container properly
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RUN mkdir -p /root/.config/matplotlib
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RUN echo "backend : Agg" > /root/.config/matplotlib/matplotlibrc

README.md

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# ![nf-core/ampliseq](docs/images/nfcore-ampliseq_logo.png)
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[![Build Status](https://github.com/nf-core/ampliseq/workflows/ampliseq%20CI/badge.svg)](https://github.com/nf-core/ampliseq/workflows/ampliseq%20CI/badge.svg)
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[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)
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[![nf-core](https://img.shields.io/badge/nf--core-pipeline-brightgreen.svg)](https://nf-co.re/)
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[![DOI](https://zenodo.org/badge/150448201.svg)](https://zenodo.org/badge/latestdoi/150448201)
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[![Cite Preprint](https://img.shields.io/badge/Cite%20Us!-Cite%20Preprint-orange)](https://biorxiv.org/cgi/content/short/2019.12.17.880468v1)
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[![GitHub Actions CI Status](https://github.com/nf-core/ampliseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/ampliseq/actions)
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[![GitHub Actions Linting Status](https://github.com/nf-core/ampliseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/ampliseq/actions)
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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
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[![Docker](https://img.shields.io/docker/automated/nfcore/ampliseq.svg)](https://hub.docker.com/r/nfcore/ampliseq)
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[![DOI](https://zenodo.org/badge/150448201.svg)](https://zenodo.org/badge/latestdoi/150448201)
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![Singularity Container available](https://img.shields.io/badge/singularity-available-7E4C74.svg)
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[![Joins us on Slack](https://img.shields.io/badge/slack-nfcore/ampliseq-blue.svg)](https://nfcore.slack.com/channels/ampliseq)
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## Introduction
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### Credits
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These scripts were originally written for use at the [Quantitative Biology Center (QBiC)](http://www.qbic.life) and [Microbial Ecology, Center for Applied Geosciences](http://www.uni-tuebingen.de/de/104325), part of Eberhard Karls Universität Tübingen (Germany) by Daniel Straub ([@d4straub](https://github.com/d4straub)) and Alexander Peltzer ([@apeltzer](https://github.com/apeltzer)).
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## Citation
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If you use nf-core/ampliseq for your analysis, please cite it using the following DOI:
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3568091.svg)](https://doi.org/10.5281/zenodo.3568091)
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The pre-print can be cited as follows:
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[![DOI](https://img.shields.io/badge/-Cite%20Preprint-orange)](https://www.biorxiv.org/content/10.1101/2019.12.17.880468v1)
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You can cite the `nf-core` pre-print as follows:
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> Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v2).

conf/base.config

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withName: make_SILVA_132_16S_classifier {
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cpus = { check_max (2 * task.attempt, 'cpus' ) }
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memory = { check_max (35.GB * task.attempt, 'memory' ) }
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time = { check_max (6.h * task.attempt, 'time' ) }
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time = { check_max (12.h * task.attempt, 'time' ) }
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}
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//max memory seen yet: 63.GB

docs/output.md

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**Output directory: `results/abundance-table/filtered`**
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* `abs-abund-table-2.tsv`
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* Tab-separated absolute abundance table at phylum level
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* `abs-abund-table-3.tsv`
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* Tab-separated absolute abundance table at class level
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* `abs-abund-table-4.tsv`
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* Tab-separated absolute abundance table at order level
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* `abs-abund-table-5.tsv`
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* Tab-separated absolute abundance table at family level
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* `abs-abund-table-6.tsv`
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* Tab-separated absolute abundance table at genus level
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* `abs-abund-table-7.tsv`
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* Tab-separated absolute abundance table at species level
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* `count_table_filter_stats.tsv`
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* Tab-separated table with information on how much counts were filtered for each sample
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* `feature-table.biom`

docs/usage.md

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* [--reads](#--reads)
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* [--FW_primer and --RV_primer](#--fw_primer-and---rv_primer)
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* [--metadata](#--metadata)
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* [----qiime_timezone](#--qiime_timezone)
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* [Other input options](#other-input-options)
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* [--extension](#--extension)
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* [--multipleSequencingRuns](#--multiplesequencingruns)
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2. The metadata file has to follow the [QIIME2 specifications](https://docs.qiime2.org/2019.10/tutorials/metadata/)
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3. In case of multiple sequencing runs, specific naming of samples are required, see [here](#--multipleSequencingRuns)
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### `--qiime_timezone`
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If a timezone error occurs, this parameter needs to be specified (default: 'Europe/Berlin'). Find your appropriate timezone with e.g. tzselect.
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Note, this affects the timezone of the entire software environment.
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## Other input options
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### `--extension`

environment.yml

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name: nf-core-ampliseq-1.1.1
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name: nf-core-ampliseq-1.1.2
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channels:
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- qiime2
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- qiime2/label/r2019.10

main.nf

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The minimal command for running the pipeline is as follows:
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nextflow run nf-core/ampliseq -profile singularity --reads "data" --FW_primer GTGYCAGCMGCCGCGGTAA --RV_primer GGACTACNVGGGTWTCTAAT
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In case of a timezone error, please specify "--qiime_timezone", e.g. --qiime_timezone 'Europe/Berlin'!
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Main arguments:
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-profile [strings] Use this parameter to choose a configuration profile. If not specified, runs locally and expects all software
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--FW_primer [str] Forward primer sequence
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--RV_primer [str] Reverse primer sequence
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--metadata [path/to/file] Path to metadata sheet, when missing most downstream analysis are skipped (barplots, PCoA plots, ...)
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--qiime_timezone [str] Needs to be specified to resolve a timezone error (default: 'Europe/Berlin')
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Other input options:
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--extension [str] Naming of sequencing files (default: "/*_R{1,2}_001.fastq.gz").
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env MATPLOTLIBRC from ch_mpl_classifier
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output:
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file("taxonomy.qza") into (ch_qiime_taxonomy_for_filter,ch_qiime_taxonomy_for_relative_abundance_reduced_taxa,ch_qiime_taxonomy_for_barplot,ch_qiime_taxonomy_for_ancom)
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file("taxonomy.qza") into (ch_qiime_taxonomy_for_filter,ch_qiime_taxonomy_for_relative_abundance_reduced_taxa,ch_qiime_taxonomy_for_barplot,ch_qiime_taxonomy_for_ancom,ch_qiime_taxonomy_for_export_filtered_dada_output)
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file("taxonomy/taxonomy.tsv") into ch_tsv_taxonomy
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saveAs: {filename ->
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if (filename.indexOf("table/feature-table.biom") == 0) "abundance_table/filtered/feature-table.biom"
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else if (filename.indexOf("table/feature-table.tsv") == 0) "abundance_table/filtered/feature-table.tsv"
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else if (filename.indexOf("abs-abund-table-") == 0) "abundance_table/filtered/$filename"
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else if (filename.indexOf("filtered/*")) "representative_sequences/$filename"
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else null}
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input:
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file table from ch_qiime_table_for_filtered_dada_output
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file repseq from ch_qiime_repseq_for_dada_output
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file taxonomy from ch_qiime_taxonomy_for_export_filtered_dada_output
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env MATPLOTLIBRC from ch_mpl_for_export_dada_output
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file("filtered/sequences.fasta") into ch_fasta_repseq
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file("table/feature-table.tsv") into (ch_tsv_table_for_alpha_rarefaction,ch_tsv_table_for_report_filter_stats,ch_tsv_table_for_diversity_core)
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file("table/feature-table.biom")
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file("filtered/*")
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file("abs-abund-table-*.tsv")
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"""
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#produce raw count table in biom format "table/feature-table.biom"
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--o-visualization rep-seqs.qzv
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qiime tools export --input-path rep-seqs.qzv \
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--output-path filtered
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##on several taxa level
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array=( 2 3 4 5 6 7 )
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for i in \${array[@]}
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do
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#collapse taxa
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qiime taxa collapse \
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--i-table ${table} \
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--i-taxonomy ${taxonomy} \
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--p-level \$i \
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--o-collapsed-table table-\$i.qza
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#export to biom
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qiime tools export --input-path table-\$i.qza \
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--output-path table-\$i
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#convert to tab separated text file
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biom convert \
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-i table-\$i/feature-table.biom \
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-o abs-abund-table-\$i.tsv --to-tsv
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done
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"""
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nextflow.config

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igenomes_base = "./iGenomes"
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tracedir = "${params.outdir}/pipeline_info"
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clusterOptions = false
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qiime_timezone = 'Europe/Berlin'
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// Defines all parameters that are independent of a test run
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trunc_qmin = 25 //to calculate params.trunclenf and params.trunclenr automatically
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reference_database = "https://www.arb-silva.de/fileadmin/silva_databases/qiime/Silva_132_release.zip"
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dereplication = 99
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// Boilerplate options
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name = false
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multiqc_config = "$baseDir/assets/multiqc_config.yaml"
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email = false
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maxMultiqcEmailFileSize = 25.MB
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plaintext_email = false
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monochrome_logs = false
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help = false
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tracedir = "${params.outdir}/pipeline_info"
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awsqueue = false
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awsregion = 'eu-west-1'
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igenomesIgnore = true
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custom_config_version = 'master'
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custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
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hostnames = false
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config_profile_description = false
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config_profile_contact = false
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config_profile_url = false
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// Boilerplate options
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name = false
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multiqc_config = "$baseDir/assets/multiqc_config.yaml"
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email = false
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maxMultiqcEmailFileSize = 25.MB
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plaintext_email = false
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monochrome_logs = false
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help = false
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tracedir = "${params.outdir}/pipeline_info"
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awsqueue = false
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awsregion = 'eu-west-1'
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igenomesIgnore = true
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custom_config_version = 'master'
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custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
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hostnames = false
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config_profile_description = false
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config_profile_contact = false
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config_profile_url = false
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}
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//export Time Zone required for QIIME2 2019.10
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env {
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TZ = params.qiime_timezone
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}
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// Load base.config by default for all pipelines
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includeConfig 'conf/base.config'
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// Container slug. Stable releases should specify release tag!
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// Developmental code should specify :dev
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process.container = 'nfcore/ampliseq:1.1.1'
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process.container = 'nfcore/ampliseq:1.1.2'
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// Load base.config by default for all pipelines
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includeConfig 'conf/base.config'
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} catch (Exception e) {
7884
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
7985
}
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// Load nf-core/ampliseq custom profiles from different Institutions
87+
try {
88+
includeConfig "${params.custom_config_base}/pipeline/ampliseq.config"
89+
} catch (Exception e) {
90+
System.err.println("WARNING: Could not load nf-core/config/ampliseq profiles: ${params.custom_config_base}/pipeline/ampliseq.config")
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}
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profiles {
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awsbatch { includeConfig 'conf/awsbatch.config' }
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homePage = 'https://github.com/nf-core/ampliseq'
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description = '16S rRNA amplicon sequencing analysis workflow using QIIME2'
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homePage = 'https://github.com/nf-core/ampliseq'
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version = '1.1.1'
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version = '1.1.2'
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mainScript = 'main.nf'
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nextflowVersion = '>=19.10.0'
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}

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