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main.nf
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#!/usr/bin/env nextflow
/*
========================================================================================
PhyloNext: GBIF phylogenetic diversity pipeline
========================================================================================
License: MIT
Github : https://github.com/vmikk/phylonext
Website: https://phylonext.github.io/
----------------------------------------------------------------------------------------
*/
// Enable DSL2 syntax
nextflow.enable.dsl = 2
// Parameters are defined in the `conf/params.config` file
// // Biodiverse args
// biodiverse_args = "function=" + params.randname + " max_iters=" + params.iterations
// How many randomization iterations should be per Biodiverse thread?
if( params.biodiversethreads > 1 ) {
randomization_chunks = (0..<params.biodiversethreads)
iterations_per_thread = params.iterations / params.biodiversethreads
iterations_per_thread = Math.ceil(iterations_per_thread).toInteger()
}
else {
randomization_chunks = [ 1 ]
iterations_per_thread = params.iterations
}
biodiverse_args = "function=" + params.randname + " max_iters=" + iterations_per_thread
// OTT-derived tree should have Latin tip names
if(params.phytree == null & params.phylabels == "OTT"){
println("No user-supplied phylogenetic tree was provided.")
println("Tree will be automatically fetched from the Open Tree of Life.")
println("!! Please set `--phylabels` parameter to `Latin`")
exit(1)
}
// Optional input files
specieskeys = params.specieskeys ? file(params.specieskeys) : file("${params.outdir}/no_file0")
noextinct = params.noextinct ? file(params.noextinct) : file("${params.outdir}/no_file1")
terrestrial = params.terrestrial ? file(params.terrestrial) : file("${params.outdir}/no_file2")
rmcountrycentroids = params.rmcountrycentroids ? file(params.rmcountrycentroids) : file("${params.outdir}/no_file3")
rmcountrycapitals = params.rmcountrycapitals ? file(params.rmcountrycapitals) : file("${params.outdir}/no_file4")
rminstitutions = params.rminstitutions ? file(params.rminstitutions) : file("${params.outdir}/no_file5")
rmurban = params.rmurban ? file(params.rmurban) : file("${params.outdir}/no_file6")
wgsrpd = params.wgsrpd ? file(params.wgsrpd) : file("${params.outdir}/no_file7")
phytree = params.phytree ? file(params.phytree) : file("${params.outdir}/no_file8")
world = params.world ? file(params.world) : file("${params.outdir}/no_file9")
polygon = params.polygon ? file(params.polygon) : file("${params.outdir}/no_file10")
// Pipeline help message
def helpMsg() {
log.info"""
=====================================================================
PhyloNext: GBIF phylogenetic diversity pipeline : Version ${workflow.manifest.version}
=====================================================================
Pipeline Usage:
To run the pipeline, enter the following in the command line:
nextflow run vmikk/phylonext -r main --input ... --outdir ...
Options:
REQUIRED:
--input Path to the directory with parquet files (GBIF occurrcence dump)
--outdir The output directory where the results will be saved
OPTIONAL:
--phylum Phylum to analyze (multiple comma-separated values allowed); e.g., "Chordata"
--classis Class to analyze (multiple comma-separated values allowed); e.g., "Mammalia"
--order Order to analyze (multiple comma-separated values allowed); e.g., "Carnivora"
--family Family to analyze (multiple comma-separated values allowed); e.g., "Felidae,Canidae"
--genus Genus to analyze (multiple comma-separated values allowed); e.g., "Felis,Canis,Lynx"
--specieskeys Custom list of GBIF specieskeys (file with a single column, with header)
--phytree Custom phylogenetic tree
--taxgroup Specific taxonomy group in Open Tree of Life (default, "All_life")
--phylabels Type of tip labels on a phylogenetic tree ("OTT" or "Latin")
--maxage Manually assign root age for a tree obtained from Open Tree of Life; e.g., 127
--phyloonly Prune Open Tree tips for which there are no phylogenetic inputs; logical, default, false
--country Country code, ISO 3166 (multiple comma-separated values allowed); e.g., "DE,PL,CZ"
--latmin Minimum latitude of species occurrences (decimal degrees); e.g., 5.1
--latmax Maximum latitude of species occurrences (decimal degrees); e.g., 15.5
--lonmin Minimum longitude of species occurrences (decimal degrees); e.g., 47.0
--lonmax Maximum longitude of species occurrences (decimal degrees); e.g., 55.5
--minyear Minimum year of record's occurrences; default, 1945
--maxyear Maximum year of record's occurrences; default, none
--coordprecision Coordinate precision threshold (less than maximum allowed value; default, 0.1)
--coorduncertainty Maximum allowed coordinate uncertainty, meters (default, 10000)
--coorduncertaintyexclude Black list of coordinate uncertainty values (default, "301,3036,999,9999")
--basisofrecordinclude Basis of record to include from the data; e.g., "PRESERVED_SPECIMEN"
--basisofrecordexclude Basis of record to exclude from the data; e.g., "FOSSIL_SPECIMEN,LIVING_SPECIMEN"
--polygon Custom area of interest (a file with polygons in GeoPackage format)
--wgsrpd Polygons of World Geographical Regions; e.g., "pipeline_data/WGSRPD.RData"
--regions Names of World Geographical Regions; e.g., "L1_EUROPE,L1_ASIA_TEMPERATE"
--noextinct File with extinct species specieskeys for their removal (file with a single column, with header)
--excludehuman Logical, exclude genus "Homo" from occurrence data (default, true)
--roundcoords Numeric, round spatial coordinates to N decimal places, to reduce the dataset size (default, 2; set to negative to disable rounding)
--h3resolution Spatial resolution of the H3 geospatial indexing system; e.g., 4
--dbscan Logical, remove spatial outliers with density-based clustering; e.g., "false"
--dbscannoccurrences Minimum species occurrence to perform DBSCAN; e.g., 30
--dbscanepsilon DBSCAN parameter epsilon, km; e.g., "700"
--dbscanminpts DBSCAN min number of points; e.g., "3"
--terrestrial Land polygon for removal of non-terrestrial occurrences; e.g., "pipeline_data/Land_Buffered_025_dgr.RData"
--rmcountrycentroids Polygons with country and province centroids; e.g., "pipeline_data/CC_CountryCentroids_buf_1000m.RData"
--rmcountrycapitals Polygons with country capitals; e.g., "pipeline_data/CC_Capitals_buf_10000m.RData"
--rminstitutions Polygons with biological institutuions and museums; e.g., "pipeline_data/CC_Institutions_buf_100m.RData"
--rmurban Polygons with urban areas; e.g., "pipeline_data/CC_Urban.RData"
--deriveddataset Prepare a list of DOIs for the datasets used (default, true)
--indices Comma-seprated list of diversity and endemism indices; e.g., "calc_richness,calc_pd,calc_pe"
--randname Randomisation scheme type; e.g., "rand_structured"
--iterations Number of randomisation iterations; e.g., 1000
--biodiversethreads Number of Biodiverse threads; e.g., 10
--randconstrain Polygons to perform spatially constrained randomization (GeoPackage format)
Leaflet interactive visualization:
--leaflet_var Variables to plot; e.g., "RICHNESS_ALL,PD,SES_PD,PD_P,ENDW_WE,SES_ENDW_WE,PE_WE,SES_PE_WE,CANAPE,Redundancy"
--leaflet_canapesuper Include the `superendemism` class in CANAPE results (default, false)
--leaflet_color Color scheme for continuous variables (default, "RdYlBu")
--leaflet_palette Color palette for continuous variables (default, "quantile")
--leaflet_bins Number of color bins for continuous variables (default, 5)
--leaflet_sescolor Color scheme for standardized effect sizes, SES (default, "threat"; alternative - "hotspots)
--leaflet_redundancy Redundancy threshold for hiding the grid cells with low number of records (default, 0 = display all grid cells)
--leaflet_zoom Zoom factor of the image for Leaflet-based screenshots (default, 2)
--leaflet_width Image width of Leaflet-based screenshots (default, 3840)
--leaflet_height Image height of Leaflet-based screenshots (default, 2160)
Static visualization:
--plotvar Variables to plot (multiple comma-separated values allowed); e.g., "RICHNESS_ALL,PD,PD_P"
--plottype Plot type
--plotformat Plot format (jpg,pdf,png)
--plotwidth Plot width (default, 18 inches)
--plotheight Plot height (default, 18 inches)
--plotunits Plot size units (in,cm)
--world World basemap
NEXTFLOW-SPECIFIC:
-qs Queue size (max number of processes that can be executed in parallel); e.g., 8
-w Path to the working directory to store intermediate results (default, "./work")
-resume Execute the pipeline using the cached results.<br>Useful to continue executions that was stopped by an error
-profile Configuration profile; e.g., "docker"
-params-file Parameter file in YAML or JSON format (e.g., "Mammals.yaml")
-c / -C Configuration file (`-C` ignores all default values) (default, "nextflow.config")
""".stripIndent()
}
// Show help msg
if (params.helpMsg | params.help){
helpMsg()
exit(0)
}
// Check if input path was provided
if (params.input == null) {
println( "Please provide the directory with input data with `--input`")
exit(1)
}
// Print the parameters to the console and to the log
log.info """
====================================================================
PhyloNext: GBIF phylogenetic diversity pipeline, Version ${workflow.manifest.version}
====================================================================
GBIF occurrence dump: ${params.input}
Output path: ${params.outdir}
Launch directory: ${workflow.launchDir}
Working directory: ${workflow.workDir}
"""
.stripIndent()
log.info "===================================================================="
log.info "\n"
// Occurrence filtering, stage I
process occ_filter {
label "container_r"
queue "custom_pool"
publishDir "$params.outdir/00.Filtered1.parquet", mode: 'copy'
// cpus 10
input:
path(input)
path(noextinct)
path(polygon)
path(wgsrpd)
output:
path "Partition_low", emit: part_low, type: "dir", optional: true
path "Partition_high", emit: part_high, type: "dir", optional: true
path "spp.txt", emit: spp
path "SpeciesCounts.txt", emit: spp_all
script:
filter_specieskeys = params.specieskeys ? "--specieskeys $specieskeys" : ""
filter_extinct = params.noextinct ? "--noextinct $noextinct" : ""
filter_polygon = params.polygon ? "--polygon $polygon" : ""
filter_wgsrpd = params.wgsrpd ? "--wgsrpd $wgsrpd --regions ${params.regions}" : ""
"""
10_Filter_occurrences.R \
--input ${input} \
--phylum ${params.phylum} \
--class ${params.classis} \
--order ${params.order} \
--family ${params.family} \
--genus ${params.genus} \
--country ${params.country} \
--latmin ${params.latmin} \
--latmax ${params.latmax} \
--lonmin ${params.lonmin} \
--lonmax ${params.lonmax} \
--minyear ${params.minyear} \
--maxyear ${params.maxyear} \
--coordprecision ${params.coordprecision} \
--coorduncertainty ${params.coorduncertainty} \
--coorduncertaintyexclude ${params.coorduncertaintyexclude} \
--basisofrecordinclude ${params.basisofrecordinclude} \
--basisofrecordexclude ${params.basisofrecordexclude} \
${filter_specieskeys} \
${filter_extinct} \
${filter_polygon} \
${filter_wgsrpd} \
--excludehuman ${params.excludehuman} \
--roundcoords ${params.roundcoords} \
--threads ${task.cpus} \
--noccurrences ${params.dbscannoccurrences} \
--output "."
## Prepare species list for DBSCAN
awk '\$3 ~ /high/ {print \$1 }' SpeciesCounts.txt > spp.txt
## Remove `equal` sign (causes a problem with azcopy)
mv 'Partition=low' Partition_low
mv 'Partition=high' Partition_high
## Check the size of output directories, if empty - remove them
if [ -d 'Partition_low' ]; then rmdir --ignore-fail-on-non-empty 'Partition_low' ; fi
if [ -d 'Partition_high' ]; then rmdir --ignore-fail-on-non-empty 'Partition_high' ; fi
"""
}
// Counting the total number of records per H3 cell ("sampling effort" for the redundancy estimator)
process record_count {
label "container_r"
queue "custom_pool"
publishDir "$params.outdir/01.NumRecords", mode: 'copy'
// cpus 10
input:
path(input)
path(noextinct)
path(polygon)
path(wgsrpd)
path(terrestrial)
path(rmcountrycentroids)
path(rmcountrycapitals)
path(rminstitutions)
path(rmurban)
output:
path "Record_counts_H3.RData", emit: n_recr
path "Record_counts_H3.txt.gz", emit: n_rect
path "Record_counts_H3_PerSpecies.RData", emit: n_spr
path "Record_counts_H3_PerSpecies.txt.gz", emit: n_spt
path "Record_counts_Outliers.txt.gz", emit: n_outl, optional: true
script:
filter_specieskeys = params.specieskeys ? "--specieskeys $specieskeys" : ""
filter_extinct = params.noextinct ? "--noextinct $noextinct" : ""
filter_polygon = params.polygon ? "--polygon $polygon" : ""
filter_terrestrial = params.terrestrial ? "--terrestrial $terrestrial" : ""
filter_country = params.rmcountrycentroids ? "--rmcountrycentroids $rmcountrycentroids" : ""
filter_capitals = params.rmcountrycapitals ? "--rmcountrycapitals $rmcountrycapitals" : ""
filter_institutions = params.rminstitutions ? "--rminstitutions $rminstitutions" : ""
filter_urban = params.rmurban ? "--rmurban $rmurban" : ""
filter_wgsrpd = params.wgsrpd ? "--wgsrpd $wgsrpd --regions ${params.regions}" : ""
"""
10_Record_counts.R \
--input ${input} \
--phylum ${params.phylum} \
--class ${params.classis} \
--order ${params.order} \
--family ${params.family} \
--genus ${params.genus} \
--country ${params.country} \
--latmin ${params.latmin} \
--latmax ${params.latmax} \
--lonmin ${params.lonmin} \
--lonmax ${params.lonmax} \
--minyear ${params.minyear} \
--maxyear ${params.maxyear} \
--coordprecision ${params.coordprecision} \
--coorduncertainty ${params.coorduncertainty} \
--coorduncertaintyexclude ${params.coorduncertaintyexclude} \
--basisofrecordinclude ${params.basisofrecordinclude} \
--basisofrecordexclude ${params.basisofrecordexclude} \
${filter_specieskeys} \
${filter_extinct} \
--excludehuman ${params.excludehuman} \
${filter_polygon} \
${filter_wgsrpd} \
${filter_terrestrial} \
${filter_country} \
${filter_capitals} \
${filter_institutions} \
${filter_urban} \
--roundcoords ${params.roundcoords} \
--resolution ${params.h3resolution} \
--threads ${task.cpus} \
--rcode \$(which "Shapefile_filters.R") \
--output "Record_counts"
"""
}
// Outlier filtering, stage II - without DBSCAN, all low abundant species
process outl_low {
label "container_r"
queue "custom_pool"
publishDir "$params.outdir/01.Filtered2_by_species", mode: 'copy'
// cpus 5
input:
path(part_low)
path(polygon)
path(wgsrpd)
path(terrestrial)
path(rmcountrycentroids)
path(rmcountrycapitals)
path(rminstitutions)
path(rmurban)
output:
path "NoSpKey.RData", emit: lowabsp, optional: true
path "NoSpKey_OutlierCounts.txt", emit: outlierslow, optional: true
script:
filter_polygon = params.polygon ? "--polygon $polygon" : ""
filter_terrestrial = params.terrestrial ? "--terrestrial $terrestrial" : ""
filter_country = params.rmcountrycentroids ? "--rmcountrycentroids $rmcountrycentroids" : ""
filter_capitals = params.rmcountrycapitals ? "--rmcountrycapitals $rmcountrycapitals" : ""
filter_institutions = params.rminstitutions ? "--rminstitutions $rminstitutions" : ""
filter_urban = params.rmurban ? "--rmurban $rmurban" : ""
filter_wgsrpd = params.wgsrpd ? "--wgsrpd $wgsrpd --regions ${params.regions}" : ""
"""
11_Additional_filtering_and_aggregation.R \
--input "${part_low}" \
--dbscan false \
--resolution ${params.h3resolution} \
${filter_polygon} \
${filter_wgsrpd} \
${filter_terrestrial} \
${filter_country} \
${filter_capitals} \
${filter_institutions} \
${filter_urban} \
--threads ${task.cpus} \
--rcode \$(which "Shapefile_filters.R") \
--output "."
"""
}
// Outlier filtering, stage II - with DBSCAN, independently by species
process outl_high {
label "container_r"
queue "custom_pool"
publishDir "$params.outdir/01.Filtered2_by_species", mode: 'copy'
// cpus 1
// Add species ID to the log file
tag "$sp"
// Iterate for each species from `species_ch` channel
input:
val sp
path(part_high)
path(polygon)
path(wgsrpd)
path(terrestrial)
path(rmcountrycentroids)
path(rmcountrycapitals)
path(rminstitutions)
path(rmurban)
output:
path "${sp}.RData", emit: sp, optional: true
path "${sp}_OutlierCounts.txt", emit: outliers, optional: true
script:
filter_polygon = params.polygon ? "--polygon $polygon" : ""
filter_terrestrial = params.terrestrial ? "--terrestrial $terrestrial" : ""
filter_country = params.rmcountrycentroids ? "--rmcountrycentroids $rmcountrycentroids" : ""
filter_capitals = params.rmcountrycapitals ? "--rmcountrycapitals $rmcountrycapitals" : ""
filter_institutions = params.rminstitutions ? "--rminstitutions $rminstitutions" : ""
filter_urban = params.rmurban ? "--rmurban $rmurban" : ""
filter_wgsrpd = params.wgsrpd ? "--wgsrpd $wgsrpd --regions ${params.regions}" : ""
"""
11_Additional_filtering_and_aggregation.R \
--input "${part_high}" \
--specieskey ${sp} \
--dbscan ${params.dbscan} \
--epsilon ${params.dbscanepsilon} \
--minpts ${params.dbscanminpts} \
--resolution ${params.h3resolution} \
${filter_polygon} \
${filter_wgsrpd} \
${filter_terrestrial} \
${filter_country} \
${filter_capitals} \
${filter_institutions} \
${filter_urban} \
--threads ${task.cpus} \
--rcode \$(which "Shapefile_filters.R") \
--output "."
"""
}
// // Create a file with paths to all chunks with filtered results
// // If there are a lot of files - it triggers and error:
// // String too long. The given string is 265799 Unicode code units long, but only a maximum of 65535 is allowed.
// process filtered_filelist {
//
// // container image is required for Cloud only
// label "container_r"
//
// input:
// val spp
//
// output:
// path "filtered_results.txt", emit: FLT
//
// shell:
// $/
// echo "${spp}" \
// | sed -z 's/, /\n/g; s/^\[//; s/\]//' \
// > filtered_results.txt
// /$
// }
// Prepare a list of OpenTree IDs (to obtain a phylogenetic tree)
process prep_ott_ids {
label "container_r"
queue "custom_pool"
publishDir "$params.outdir/02.OTT_tree", mode: 'copy'
// cpus 1
input:
path spp_all
output:
path "Species_OTT.csv", emit: spp_ott
script:
"""
11_GBIF_SpeciesKey_to_OTTID.R \
--input ${spp_all} \
--taxgroup ${params.taxgroup} \
--threads ${task.cpus} \
--output "Species_OTT.csv"
"""
}
// Get an induced subtree from synthetic phylogenetic tree for a set of OpenTree IDs
process get_ott_tree {
label "container_ott"
queue "custom_pool"
publishDir "$params.outdir/02.OTT_tree", mode: 'copy'
// publishDir "$params.tracedir", pattern: "citations.txt", mode: 'copy', saveAs: { filename -> "OTT_tree_citations.txt" }
// cpus 1
input:
path spp_ott
output:
path "ott_label_dated_tree.tre", emit: tree
path "ottid_dated_tree.tre", emit: treedated
path "labelled_tree.tre", emit: treelabeled
path "ottlabel.txt", emit: labels
path "conflict_annot.tre", emit: conflicts, optional: true
path "support_annot.tre", emit: support, optional: true
path "citations.txt"
path "date_citations.txt"
path "synth.log"
script:
max_age = params.maxage ? "--max-age ${params.maxage}" : ""
phylo_only = params.phyloonly ? "--phylo-only" : ""
"""
induced_synth_subtree_from_csv.py \
--query ${spp_ott} \
--output_dir "\$(pwd)" \
--label_format "name" \
${max_age} \
${phylo_only}
"""
}
// Merge filtered species occurrences and prep data for Biodiverse
// Add record counts (taking into account DBSCAN-based outliers)
process merge_occ {
label "container_r"
queue "custom_pool"
publishDir "$params.outdir/02.Biodiverse_input", mode: 'copy'
// cpus 10
input:
path(spp, stageAs: "FilteredData/*")
path phytree
path counts
output:
path "H3_GridCell_Centres.csv", emit: h3coords
path "Trimmed_occurrences.csv", emit: occurrences
path "Trimmed_tree.nex", emit: tree
path "Trimmed_tree.nwk", emit: treenwk
script:
"""
12_Prepare_Biodiverse_input.R \
--input "FilteredData" \
--phytree ${phytree} \
--phylabels ${params.phylabels} \
--taxgroup ${params.taxgroup} \
--counts ${counts} \
--threads ${task.cpus} \
--output "."
# --inputfile ${spp} \
"""
// Nextflow gets the names of the input files from `spp` (`flt_ch` channel)
// and copies/symlinks them to the current dir --> `--input` arg = current dir
}
// Prepare a list of DOIs for the GBIF datasets
// Acrivated by `--deriveddataset` param
process derived_datasets {
label "container_r"
queue "custom_pool"
publishDir "$params.tracedir", mode: 'copy'
// cpus 1
input:
path(input)
path(noextinct)
path(polygon)
path(wgsrpd)
path(terrestrial)
path(rmcountrycentroids)
path(rmcountrycapitals)
path(rminstitutions)
path(rmurban)
path(speciesinphylotree)
output:
path "Dataset_DOIs.txt", emit: doi
script:
filter_specieskeys = params.specieskeys ? "--specieskeys $specieskeys" : ""
filter_extinct = params.noextinct ? "--noextinct $noextinct" : ""
filter_polygon = params.polygon ? "--polygon $polygon" : ""
filter_terrestrial = params.terrestrial ? "--terrestrial $terrestrial" : ""
filter_country = params.rmcountrycentroids ? "--rmcountrycentroids $rmcountrycentroids" : ""
filter_capitals = params.rmcountrycapitals ? "--rmcountrycapitals $rmcountrycapitals" : ""
filter_institutions = params.rminstitutions ? "--rminstitutions $rminstitutions" : ""
filter_urban = params.rmurban ? "--rmurban $rmurban" : ""
filter_wgsrpd = params.wgsrpd ? "--wgsrpd $wgsrpd --regions ${params.regions}" : ""
"""
16_Derived_dataset.R \
--input ${input} \
--phylum ${params.phylum} \
--class ${params.classis} \
--order ${params.order} \
--family ${params.family} \
--genus ${params.genus} \
--country ${params.country} \
--latmin ${params.latmin} \
--latmax ${params.latmax} \
--lonmin ${params.lonmin} \
--lonmax ${params.lonmax} \
--minyear ${params.minyear} \
--maxyear ${params.maxyear} \
--coordprecision ${params.coordprecision} \
--coorduncertainty ${params.coorduncertainty} \
--coorduncertaintyexclude ${params.coorduncertaintyexclude} \
--basisofrecordinclude ${params.basisofrecordinclude} \
--basisofrecordexclude ${params.basisofrecordexclude} \
${filter_specieskeys} \
--speciestree ${speciesinphylotree} \
${filter_extinct} \
--excludehuman ${params.excludehuman} \
${filter_polygon} \
${filter_wgsrpd} \
${filter_terrestrial} \
${filter_country} \
${filter_capitals} \
${filter_institutions} \
${filter_urban} \
--roundcoords ${params.roundcoords} \
--resolution ${params.h3resolution} \
--threads ${task.cpus} \
--rcode \$(which "Shapefile_filters.R") \
--output "Dataset_DOIs.txt"
"""
}
// // Split dataset based on spatial constraints
// process split_by_polygons {
//
// label "container_r"
// queue "custom_pool"
//
// publishDir "$params.outdir/02.Biodiverse_input", mode: 'copy'
// // cpus 2
//
// input:
// path occurrences
// path polygons
//
// output:
// path "SpatConstrained_*.csv", emit: occsplit
//
// script:
// """
//
// 12_Split_dataset_SpatialConstraints.R \
// --input ${occurrences} \
// --randconstrain ${polygons} \
// --threads ${task.cpus} \
// --output "SpatConstrained_"
//
// """
// }
// Create Biodiverse input files
process prep_biodiv {
label "container_biodiverse"
queue "custom_pool"
publishDir "$params.outdir/02.Biodiverse_input", mode: 'copy'
// cpus 1
input:
path occurrences
path tree
output:
path "occ.bds", emit: BDS
path "tree.bts", emit: BTS
path "occ_analysed.bds", emit: BDA
path "occ.bds.csv", emit: BDOBS
script:
"""
## For debugging - check which Perl are we using?
# perl --version
## Prepare Biodiverse input file
## NB! column numbers are zero-based here
## Latitude = Y, Longitude = X
00_create_bds.pl \
--csv_file ${occurrences} \
--out_file "occ.bds" \
--label_column_number '0' \
--sampcount_column_number '6' \
--group_column_number_x '5' \
--group_column_number_y '4' \
--cell_size_x '0' \
--cell_size_y '0'
## Prepare the tree for Biodiverse
00_create_bts.pl \
--input_tree_file ${tree} \
--out_file "tree.bts"
## Run the analyses
02_biodiverse_analyses.pl \
--input_bds_file "occ.bds" \
--input_bts_file "tree.bts" \
--calcs ${params.indices}
"""
}
// Estimate phylogenetic diversity with Biodiverse
process phylodiv {
label "container_biodiverse"
queue "custom_pool"
// publishDir "$params.outdir/02.Biodiverse_results", mode: 'copy'
// cpus 1
input:
path(BDA)
val(chunkid)
output:
path "Biodiv_randomized_${chunkid}.bds", emit: BDArand
script:
"""
03_run_randomisation.pl \
--basedata ${BDA} \
--bd_name ${BDA} \
--out_file "Biodiv_randomized.bds" \
--rand_name 'rand' \
--iterations ${iterations_per_thread} \
--args ${biodiverse_args} \
seed=${chunkid}
## Add chunk ID into the file name
mv "Biodiv_randomized.bds" "Biodiv_randomized_${chunkid}.bds"
"""
}
// Prepare a shapefile to spatially constrain randomizations
process prep_shapefile {
label "container_r"
queue "custom_pool"
// cpus 1
input:
path(occurrences)
path(polygons)
output:
path "shapefile*", emit: shapefile
script:
"""
12_Prepare_SpatialConstraints.R \
--input ${occurrences} \
--randconstrain ${polygons} \
--threads ${task.cpus} \
--output "shapefile"
"""
}
// Estimate phylogenetic diversity using spatially-constrained randomizations
process phylodiv_constrianed {
label "container_biodiverse"
queue "custom_pool"
// publishDir "$params.outdir/02.Biodiverse_results", mode: 'copy'
// cpus 1
input:
path(BDA)
path(polygons)
val(chunkid)
output:
path "Biodiv_randomized_${chunkid}.bds", emit: BDArand
script:
"""
03_run_randomisation.pl \
--basedata ${BDA} \
--bd_name ${BDA} \
--out_file "Biodiv_randomized.bds" \
--rand_name 'rand' \
--iterations ${iterations_per_thread} \
--args ${biodiverse_args} \
seed=${chunkid} \
spatial_conditions_for_subset='sp_points_in_same_poly_shape (file => "shapefile.shp")'
## Add chunk ID into the file name
mv "Biodiv_randomized.bds" "Biodiv_randomized_${chunkid}.bds"
"""
}
// Create a file with paths to all chunks with randomization results
process rand_filelist {
// container image is required for Cloud only
label "container_r"
queue "custom_pool"
input:
path(randfiles)
//// To avoid name collisions if analysis was done for multiple datasets
// path(randfiles, stageAs: "?/*")
output:
path "randomization_results.txt", emit: RND
shell:
$/
echo "${randfiles}" \
| sed -z 's/, /\n/g; s/^\[//; s/\]//' \
> randomization_results.txt
/$
}
// Groovy allows an alternative syntax for string definitions
// which uses the $ as escape character in place of \ character.
// These strings are delimited with an opening $/ and and a closing /$
// Aggregate the randomization results - with Biodiverse
process aggregate_rnds_biodiv {
label "container_biodiverse"
queue "custom_pool"
publishDir "$params.outdir/02.Biodiverse_results", mode: 'copy'
// cpus 1
input:
path RND
path BDArand
output:
path "Biodiverse.bds", emit: Biodiv
script:
"""
05_reintegrate_basedatas_post_rand.pl \
--glob ${RND} \
--output_prefix Biodiverse
"""
}
// Export Biodiverse results into CSV
process div_to_csv {
label "container_biodiverse"
queue "custom_pool"
publishDir "$params.outdir/02.Biodiverse_results", mode: 'copy'
// cpus 1
input:
path Biodiv
output:
path "RND_groups.csv", emit: grp
path "RND_SPATIAL_RESULTS.csv", emit: spat
path "RND_rand--SPATIAL_RESULTS.csv", emit: spat_r
path "RND_rand--p_rank--SPATIAL_RESULTS.csv", emit: spat_p
path "RND_rand--z_scores--SPATIAL_RESULTS.csv", emit: spat_z
path "RND_rand--CANAPE--.csv", emit: canape, optional: true
path "RND_HURLBERT_ES.csv", emit: hurl, optional: true
path "RND_rand--HURLBERT_ES.csv", emit: hurl_r, optional: true
path "RND_rand--p_rank--HURLBERT_ES.csv", emit: hurl_p, optional: true
path "RND_rand--z_scores--HURLBERT_ES.csv", emit: hurl_z, optional: true
script:
"""
04_load_bds_and_export_results.pl \
--input_bds_file ${Biodiv} \
--output_csv_prefix 'RND'
"""
}
// Plot Biodiverse results
process plot_pd {
label "container_r"
queue "custom_pool"
publishDir "$params.outdir/03.Plots", mode: 'copy'
input:
path BDOBS // observed indices
path spat_z // randomized indices
path world
output:
path "*.${params.plotformat}"
script:
add_world_map = params.world ? "--world $world" : ""
"""
14_Visualization.R \
--observed ${BDOBS} \
--zscores ${spat_z} \
--threads ${task.cpus} \
--variables ${params.plotvar} \
--resolution ${params.h3resolution} \
${add_world_map} \
--format "${params.plotformat}" \
--plotz "${params.plottype}" \
--width "${params.plotwidth}" \
--height "${params.plotheight}" \
--units "${params.plotunits}" \
--output "."
"""
}
// Plot PD indices (interactive map - Leaflet-based choropleth)
process plot_leaflet {
label "container_r"
queue "custom_pool"
publishDir "$params.outdir/03.Plots", mode: 'copy'
input:
path BDOBS // observed indices
path spat_z // randomized indices
path spat_r // randomization-based p-values
path NRECORDS // number of raw records per grid cell
path canape // CANAPE results
path hurl // Hurlbert ES indices
output:
path "Choropleth.html"
path "Choropleth_files", optional: true
path "Biodiverse_results_merged.txt", optional: true, emit: tab
path "Diversity_estimates.gpkg", emit: geopackage
path "Leaflet_object.RData", emit: leaflet
script:
"""
15_Leaflets.R \
--observed ${BDOBS} \
--sesscores ${spat_z} \
--sigscores ${spat_r} \
--canape ${canape} \
--hurlbert ${hurl} \
--reccounts ${NRECORDS} \