"""
q2_import.sh ${params.singleEnd} ${q2_manifest} data.qza data.qzv import_output completecmd &> q2_import.log 2>&1
qiime --version|grep 'q2cli'|cut -d' ' -f3 > v_qiime2.txt
"""

"""
cut -d \$'\t' -f1 ${decontam_table} | sed '1d' > decontaminated_ASV_ID.txt
seqtk subseq ${dada2_output}/sequences.fasta decontaminated_ASV_ID.txt > decontaminated_ASV.fasta
"""

"""
minimap2 -t ${task.cpus} -K 25M -ax ${params.lr_type} -L ${params.lr_tax_fna} ${fastq} | samtools view -h -F0xe00 | samtools sort -o ${sample}.bam -O bam - &> lr_minimap2.log 2>&1
touch lr_mapping.ok
samtools index ${sample}.bam &> lr_samtools-sort.log 2>&1
touch lr_samtools-sort.ok
minimap2 --version > v_minimap2.txt
"""

"""
if [ ${params.longreads} = "true" ];
then
    Rscript --vanilla ${baseDir}/bin/create_phyloseq_obj_longreads.R phyloseq.rds ${biom_tsv} ${metadata} ${params.lr_rank} ${params.kingdom} table_with_taxo_for_stats.tsv &>> stats_prepare_data_lr.log 2&>1
else
    prepare_data_for_stats.sh ${metadata} ${biom_tsv} table_with_taxo_for_stats.tsv metadata_stats.tsv ${params.microDecon_enable} ${params.stats_only} &> stats_prepare_data.log 2&>1
    Rscript --vanilla ${baseDir}/bin/create_phyloseq_obj.R phyloseq.rds table_with_taxo_for_stats.tsv metadata_stats.tsv ${params.microDecon_enable} ${params.control_list} ${newick_tree} ${params.remove_sample} ${params.sample_to_remove} &>> stats_prepare_data.log 2&>1
fi
## get statistics libraries version for report
Rscript -e "write(x=as.character(paste0(R.Version()[c('major','minor')], collapse = '.')), file='v_R.txt')"
Rscript -e "library(dplyr); write(x=as.character(packageVersion('dplyr')), file='v_dplyr.txt')"
Rscript -e "library(stringr); write(x=as.character(packageVersion('stringr')), file='v_stringr.txt')"
Rscript -e "library(phyloseq); x=as.character(packageVersion('phyloseq')); write(x, file='v_phyloseq.txt')"
Rscript -e "library(phangorn); write(x=as.character(packageVersion('phangorn')), file='v_phangorn.txt')"
Rscript -e "library(ggplot2); write(x=as.character(packageVersion('ggplot2')), file='v_ggplot2.txt')"
Rscript -e "library(svglite); write(x=as.character(packageVersion('svglite')), file='v_svglite.txt')"
Rscript -e "library(vegan); write(x=as.character(packageVersion('vegan')), file='v_vegan.txt')"
Rscript -e "library(RColorBrewer); write(x=as.character(packageVersion('RColorBrewer')), file='v_RColorBrewer.txt')"
Rscript -e "library(tidyr); write(x=as.character(packageVersion('tidyr')), file='v_tidyr.txt')"
Rscript -e "library(gridExtra); write(x=as.character(packageVersion('gridExtra')), file='v_gridExtra.txt')"
Rscript -e "library(egg); write(x=as.character(packageVersion('egg')), file='v_egg.txt')"
Rscript -e "library(reshape2); write(x=as.character(packageVersion('reshape2')), file='v_reshape2.txt')"
Rscript -e "library(BiocManager); write(x=as.character(packageVersion('BiocManager')), file='v_BiocManager.txt')"
Rscript -e "library(microbiome); write(x=as.character(packageVersion('microbiome')), file='v_microbiome.txt')"
Rscript -e "library(dendextend); write(x=as.character(packageVersion('dendextend')), file='v_dendextend.txt')"
Rscript -e "library(metagenomeSeq); write(x=as.character(packageVersion('metagenomeSeq')), file='v_metagenomeSeq.txt')"
Rscript -e "library(DESeq2); write(x=as.character(packageVersion('DESeq2')), file='v_DESeq2.txt')"
Rscript -e "library(UpSetR); write(x=as.character(packageVersion('UpSetR')), file='v_UpSetR.txt')"
touch 'version_ok'
"""

"""
#!/usr/bin/env python
import os, json
from shutil import copyfile

data = {}
data["projectName"] = '$params.projectName'
data["run_date"] = '$date'
data["singleEnd"] = '$params.singleEnd'
data["manifest"] = '$params.input_manifest'
data["metadata"] = '$params.input_metadata'
data["outdir"] = '$params.outdir'
data["steps"] = {}
data["steps"]["data_integrity_enable"] = '$params.data_integrity_enable'
data["steps"]["cutadapt_enable"] = '$params.cutadapt_enable'
data["steps"]["dbotu3_enable"] = '$params.dbotu3_enable'
data["steps"]["filtering_tax_enable"] = '$params.filtering_tax_enable'
data["steps"]["microDecon_enable"] = '$params.microDecon_enable'
data["steps"]["ancom_enable"] = '$params.ancom_enable'
data["steps"]["picrust2_enable"] = '$params.picrust2_enable'
data["steps"]["stats_alpha_enable"] = '$params.stats_alpha_enable'
data["steps"]["stats_beta_enable"] = '$params.stats_beta_enable'
data["steps"]["stats_desc_comp_enable"] = '$params.stats_desc_comp_enable'
data["steps"]["report_enable"] = '$params.report_enable'
data["steps"]["stats_only"] = '$params.stats_only'
data["steps"]["dada2merge"] = '$params.dada2merge'
data["steps"]["longreads"] = '$params.longreads'

data["integrity"] = {}
data["integrity"]["primer_filter"] = '$params.primer_filter' or None

data["cutadapt"] = {}
data["cutadapt"]["primerF"] = '$params.primerF' or None
data["cutadapt"]["primerR"] = '$params.primerR' or None
data["cutadapt"]["errorRate"] = '$params.errorRate' or None
data["cutadapt"]["overlap"] = '$params.overlap' or None

data["dada2"] = {}
data["dada2"]["FtrimLeft"] = '$params.FtrimLeft' or None
data["dada2"]["RtrimLeft"] = '$params.RtrimLeft' or None
data["dada2"]["FtruncLen"] = '$params.FtruncLen' or None
data["dada2"]["RtruncLen"] = '$params.RtruncLen' or None
data["dada2"]["FmaxEE"] = '$params.FmaxEE' or None
data["dada2"]["RmaxEE"] = '$params.RmaxEE' or None
data["dada2"]["minQ"] = '$params.minQ' or None
data["dada2"]["chimeras"] = '$params.chimeras' or None

data["dada2merge"] = {}
data["dada2merge"]["merge_tabledir"] = '$params.merge_tabledir' or None
data["dada2merge"]["merge_repseqsdir"] = '$params.merge_repseqsdir' or None

data["dbotu3"] = {}
data["dbotu3"]["gen_crit"] = '$params.gen_crit' or None
data["dbotu3"]["abund_crit"] = '$params.abund_crit' or None
data["dbotu3"]["pval_crit"] = '$params.pval_crit' or None

data["taxonomy"] = {}
data["taxonomy"]["database"] = '$params.database' or None
data["taxonomy"]["seqs_db"] = '$params.seqs_db' or None
data["taxonomy"]["taxo_db"] = '$params.taxo_db' or None
data["taxonomy"]["extract_db"] = '$params.extract_db'
data["taxonomy"]["confidence"] = '$params.confidence' or None

data["picrust2"] = {}
data["picrust2"]["method"] = '$params.method' or None
data["picrust2"]["nsti"] = '$params.nsti' or None

data["tax_filtering"] = {}
data["tax_filtering"]["tax_to_exclude"] = '$params.tax_to_exclude' or None

data["microdecon"] = {}
data["microdecon"]["control_list"] = '$params.control_list' or None
data["microdecon"]["nb_controls"] = '$params.nb_controls' or None
data["microdecon"]["nb_samples"] = '$params.nb_samples' or None

data["lr"] = {}
data["lr"]["lr_type"] = '$params.lr_type' or None
data["lr"]["lr_rank"] = '$params.lr_rank' or None
data["lr"]["lr_tax_fna"] = '$params.lr_tax_fna' or None
data["lr"]["lr_tax_flat"] = '$params.lr_taxo_flat' or None

data["stats"] = {}
data["stats"]["ancom_var"] = '$params.ancom_var' or None
data["stats"]["kingdom"] = '$params.kingdom' or None
data["stats"]["taxa_nb"] = '$params.taxa_nb' or None
data["stats"]["hc_method"] = '$params.hc_method' or None
data["stats"]["alpha_div_group"] = '$params.alpha_div_group' or None
data["stats"]["beta_div_var"] = '$params.beta_div_var' or None
data["stats"]["desc_comp_crit"] = '$params.desc_comp_crit' or None
data["stats"]["inasv_table"] = '$params.inasv_table' or None
data["stats"]["innewick"] = '$params.innewick' or None

#software versions
data["soft"] = {}
data["soft"]["samba"] = '$workflow.manifest.version'
data["soft"]["nextflow"] = '$workflow.nextflow.version'
for elt in os.listdir("${params.outdir}/${params.report_dirname}/version"):
    if elt.endswith(".txt"):
        f=open(os.path.join("${params.outdir}/${params.report_dirname}/version",elt),"r")
        tool_name=elt.replace("v_","").replace(".txt","")
        version=f.readline().rstrip()
        data["soft"][tool_name] = version

with open('data.json', 'w') as outfile:
   json.dump(data, outfile, sort_keys=True, indent=4)

os.system("${baseDir}/bin/SAMBAreport.py -t ${SAMBAtemplate} -p ${params.outdir}/${params.report_dirname} -c 'data.json'")
os.system("cp ${wf_image} samba_wf.png")

"""