diff --git a/config/config.html b/config/config.html index d3b31209..e0dc6e21 100644 --- a/config/config.html +++ b/config/config.html @@ -177,6 +177,7 @@

root deconvolution variants_config
Type: string Default: ""

Variants configuration used during deconvolution
Example:

var_conf.yaml

root deconvolution variants_dates
Type: string Default: ""

Variants to scan per periods (as determined with COJAC by leveraging the output of the cooc rule)
Example:

var_dates.yaml

root deconvolution out_format
Type: enum (of string) Default: "lines"

Format of the output CSV.

  • lines(default) - each variants a separate entry on a separate line.
  • columns - one column per variant

Must be one of:

  • "lines"
  • "columns"

Example:

columns
+

root deconvolution filters
Type: string Default: ""

List of filters for removing problematic mutations from tally. Some mutations might be problematic and need to be taken out – e.g. due to drop-outs in the multiplex PCR amplification, they do not show up in the data and this could be misinterpreted by LolliPop as proof of absence of a variant.
Example:

filters_preprint.yaml

root web_visualization
Type: object Default: {}

root web_visualization mem
Type: integer Default: 2000

root web_visualization time
Type: integer Default: 235

root web_visualization conda
Type: string Default: "{VPIPE_BASEDIR}/envs/visualization.yaml"

root diversity
Type: object Default: {}

root diversity mem
Type: integer Default: 2000

root diversity time
Type: integer Default: 235

root diversity conda
Type: string Default: "{VPIPE_BASEDIR}/envs/diversity_measures.yaml"

root dehuman
Type: object Default: {}

root dehuman conda
Type: string Default: "{VPIPE_BASEDIR}/envs/dehuman.yaml"

root dehuman mem
Type: integer Default: 4096

root dehuman time
Type: integer Default: 235

root dehuman threads
Type: integer Default: 4

root dehuman ref_host
Type: string Default: "references/human.fa.gz"

Host’s genome used to remove reads (e.g. human genome)

Note: if this file is absent, it is possible to fetch it from a remote server, see property ref_host_url below.
Example:

/cluster/project/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa

root dehuman ref_host_url
Type: string Default: "http://ftp.ensembl.org/pub/current_fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"

If the host’s genome specified in property ref_host isn’t present, fetch it from a remote server.

Note remember to set aside enough memory for the indexing rule, see section ref_bwa_index property mem.
Examples:

http://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
 
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.29_GRCh38.p14/GCA_000001405.29_GRCh38.p14_genomic.fna.gz
@@ -187,4 +188,4 @@

root upload checksum
Type: boolean Default: false

Generate checksum for each individual consensus sequence (if a consensus is regenerated, it will help determine whether the new file has changed content or is virtually the same as the previous).
Example:

True

root upload orig_fastq
Type: boolean Default: false

Also include the original .fastq.gz sequencing reads files from raw_data/ in the list of files to be uploaded. See property orig_cram below for a compressed version and see output dehumanized_raw_reads and section dehuman for depleting reads from the host.
Example:

True

root upload orig_cram
Type: boolean Default: false

Also include a compressed version of the original sequencing raw reads files from raw_data/. Similar to property orig_fastq above, but with reference-based compression.
Example:

True
-

root upload script
Type: string Default: "{VPIPE_BASEDIR}/scripts/prepare_upload_symlinks.sh"

Custom script that assists and prepares uploads.

It will receive the following positional parameters:

  • <OUTPUT>: the output file that must be created by the script.
  • <SAMPLE_ID>: a string (with no path separator slashes) that can be used as a name, uniquely identifying the sample and the date.
  • <SAMPLE_DIR>: the base directory of the sample.
  • <UPLOAD_FILES>…: a list of files to consider for upload

For an example, see the default script prepare_upload_symlinks.sh, it generates symlinks that help tracking which samples are new and/or updated between runs of V-pipe and thus should be considered for upload.

root upload options
Type: string Default: ""

Named options to be passed to the script, before the positional parameters. E.g. for an extra configuration file with SFTP server information.
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root upload script
Type: string Default: "{VPIPE_BASEDIR}/scripts/prepare_upload_symlinks.sh"

Custom script that assists and prepares uploads.

It will receive the following positional parameters:

  • <OUTPUT>: the output file that must be created by the script.
  • <SAMPLE_ID>: a string (with no path separator slashes) that can be used as a name, uniquely identifying the sample and the date.
  • <SAMPLE_DIR>: the base directory of the sample.
  • <UPLOAD_FILES>…: a list of files to consider for upload

For an example, see the default script prepare_upload_symlinks.sh, it generates symlinks that help tracking which samples are new and/or updated between runs of V-pipe and thus should be considered for upload.

root upload options
Type: string Default: ""

Named options to be passed to the script, before the positional parameters. E.g. for an extra configuration file with SFTP server information.
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