Snakemake Report

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Workflow

Click the nodes to obtain details about each step.

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Jobs 12

Input files

results/sh_refs_qiime_{ver}_{id}_{type}{date}_dev.qza
results/sh_taxa_qiime_{ver}_{id}_{type}{date}_dev.qza

Output files

results/unite_{ver}_{id}_{type}{date}.qza

Code

1	`qiime feature-classifier fit-classifier-naive-bayes --p-classify--chunk-size 10000 --i-reference-reads {input.ref} --i-reference-taxonomy {input.tax} --o-classifier {output}`

Jobs 12

Input files

results/sh_refs_qiime_{ver}_{id}_{type}{date}_dev.fixed.fasta

Output files

results/sh_refs_qiime_{ver}_{id}_{type}{date}_dev.qza

Code

1	`qiime tools import --type FeatureData[Sequence] --input-path {input} --output-path {output}`

Jobs 6

Output files

downloads/sh_refs_qiime_{ver}_{id}_{type}{date}_dev.fasta
downloads/sh_taxonomy_qiime_{ver}_{id}_{type}{date}_dev.txt

Code

        # 8.3	2021-05-10	Fungi	14 097	44 343	Current	https://doi.org/10.15156/BIO/1264708
        wget -qO- https://files.plutof.ut.ee/public/orig/C5/54/C5547B97AAA979E45F79DC4C8C4B12113389343D7588716B5AD330F8BDB300C9.tgz | tar xz -C downloads --strip-components 2 # sh_qiime_release_10.05.2021       # normal
        # 8.3	2021-05-10	Fungi	14 097	83 993	Current	https://doi.org/10.15156/BIO/1264763
        wget -qO- https://files.plutof.ut.ee/public/orig/B3/05/B3054DF783AC61A0C3BD0FDEB0516EC394934809AAE43CA0F3081C0A184FAA39.tgz | tar xz -C downloads --strip-components 2 # sh_qiime_release_s_10.05.2021     # add s for 97% singletons
        # 8.3	2021-05-10	All eukaryotes	14 237	96 423	Current	https://doi.org/10.15156/BIO/1264819
        wget -qO- https://files.plutof.ut.ee/public/orig/48/29/4829D91F763E20F0F4376A60AA53FC9FBE6029A7D1BDC1B45347DD64EDE5D560.tgz | tar xz -C downloads --strip-components 2 # sh_qiime_release_all_10.05.2021   # add all for Euks
        # 8.3	2021-05-10	All eukaryotes	14 237	190 888	Current	https://doi.org/10.15156/BIO/1264861
        wget -qO- https://files.plutof.ut.ee/public/orig/1D/31/1D31FA3A308BDC2FB2750D62C0AA40C5058C15405A3CC5C626CC3A3F5E3903ED.tgz | tar xz -C downloads --strip-components 2 # sh_qiime_release_s_all_10.05.2021 # and s and all for 97% Euks singletons

Jobs 12

Input files

downloads/sh_refs_qiime_{ver}_{id}_{type}{date}_dev.fasta

Output files

results/sh_refs_qiime_{ver}_{id}_{type}{date}_dev.fixed.fasta

Code

1	`awk '/^>/ {{print($0)}}; /^[^>]/ {{print(toupper($0))}}' {input} \| tr -d ' ' > {output}`

Jobs 12

Input files

downloads/sh_taxonomy_qiime_{ver}_{id}_{type}{date}_dev.txt

Output files

results/sh_taxa_qiime_{ver}_{id}_{type}{date}_dev.qza

Code

1	`qiime tools import --type FeatureData[Taxonomy] --input-format HeaderlessTSVTaxonomyFormat --input-path {input} --output-path {output}`