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annotate CSP2/docker/Makefile @ 39:93393808f415

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"planemo upload"
author rliterman
date Thu, 12 Dec 2024 13:53:15 -0500
parents 01431fa12065
children
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rliterman@0 1 .PHONY:
rliterman@0 2
rliterman@0 3 .ONESHELL:
rliterman@0 4
rliterman@0 5
rliterman@0 6
rliterman@0 7 usage: ## Show this menu
rliterman@0 8 @grep -E '^[a-zA-Z_-]+:.*?##.*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?##"}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
rliterman@0 9
rliterman@0 10 version: ## Show version and branch
rliterman@0 11 @echo "CSP2 v$${CSP2_VER}/$${CSP2_BRANCH}"
rliterman@0 12
rliterman@0 13 # ENV CSP2_VER=${CSP2_VER}
rliterman@0 14 # ENV BEDTOOLS_VER=${BEDTOOLS_VER}
rliterman@0 15 # ENV MIUMMER_VER=${MUMMER_VER}
rliterman@0 16 # ENV SKESA_VER=${SKESA_VER}
rliterman@0 17 # ENV MASH_VER=${MASH_VER}
rliterman@0 18 # ENV BBMAP_VER=${BBMAP_VER}
rliterman@0 19 # ENV PYTHON_VER=${PYTHON_VER}
rliterman@0 20
rliterman@0 21 versions: version ## Show versions of key installed depedencies
rliterman@0 22 @echo `nextflow -v`
rliterman@0 23 @echo `python3 --version` " (container says ${PYTHON_VER})"
rliterman@0 24 @echo `bedtools --version` " (container says ${BEDTOOLS_VER})"
rliterman@0 25 @echo "mummer " `mummer --version` " (container says ${MUMMER_VER})"
rliterman@0 26 @echo `skesa --version 2>&1` " (container says ${SKESA_VER})"
rliterman@0 27 @echo "mash " `mash --version` " (container says ${MASH_VER})"
rliterman@0 28 @echo `bbmap.sh --version 2>&1` " (container says ${BBMAP_VER})"
rliterman@0 29
rliterman@0 30 help: ## Show help
rliterman@0 31 @echo "Citation: CFSAN SNP Pipeline 2, v$${CSP2_VER}, Literman et al. 2024"
rliterman@0 32 @echo
rliterman@0 33 @echo "CSP2 is a Nextflow pipeline for rapid, accurate SNP distance estimation"
rliterman@0 34 @echo "from assembly data."
rliterman@0 35 @echo
rliterman@0 36 @echo "Please see: https://github.com/CFSAN-Biostatistics/CSP2"
rliterman@0 37 @echo
rliterman@0 38 @echo "CSP2 runs are managed via Nextflow, providing the user with an array of"
rliterman@0 39 @echo "customizations while also facilitating module development and additions in"
rliterman@0 40 @echo "future releases."
rliterman@0 41 @echo
rliterman@0 42 @echo "Important Note: The software continues to be focused on the analysis of"
rliterman@0 43 @echo "groups of bacterial genomes with limited evolutionary differences (<1000"
rliterman@0 44 @echo "SNPs). Testing is underway to determine how the underlying cluster"
rliterman@0 45 @echo "diversity impacts distances estimates."
rliterman@0 46 @echo
rliterman@0 47 @echo "CSP2 has two main run modes:"
rliterman@0 48 @echo "1) "Screening Mode" (screen): Used to determine whether query isolates are"
rliterman@0 49 @echo "close to a set of reference isolates (e.g., lab control strains, strains"
rliterman@0 50 @echo "related to an outbreak, etc.) Given one or more user-provided reference"
rliterman@0 51 @echo "isolates (--ref_reads; --ref_fasta), get alignment statistics and SNP"
rliterman@0 52 @echo "distances between all reference and query isolates (--reads; --fasta)"
rliterman@0 53 @echo
rliterman@0 54 @echo "2) "SNP Pipeline Mode" (snp): Used to generate pairwise distances and"
rliterman@0 55 @echo "alignments for a set of query isolates Generate pairwise SNP distances and"
rliterman@0 56 @echo "alignments for 2+ isolates (--reads; --fasta) based on comparisons to:"
rliterman@0 57 @echo
rliterman@0 58 @echo "One or more user-provided references (--ref_reads; --ref_fasta), or One or"
rliterman@0 59 @echo "more reference isolates selected by RefChooser (--n_ref)"
rliterman@0 60 @echo
rliterman@0 61 @echo "Usage: screen [options] {--fasta PATH {--reads=PATH | --forward=STR --reverse=STR} --out=PATH}"
rliterman@0 62 @echo " or snp [options] {--fasta {--reads=PATH | --forward=STR --reverse=STR} --out=PATH}"
rliterman@0 63 @echo
rliterman@0 64 @echo "Options:"
rliterman@0 65 @echo " --outroot=PATH\tBase directory to create output folder [default=$CWD] "
rliterman@0 66 @echo " --out=PATH\t\tName of the output folder to create (must not exist)"
rliterman@0 67 @echo "\t\t\t [default=CSP2_<current_datetime>]"
rliterman@0 68 @echo " --forward=STR\t\tFull file extension for forward/left reads of query"
rliterman@0 69 @echo "\t\t\t [default='_1.fastq.gz']"
rliterman@0 70 @echo " --reverse=STR\t\tFull file extension for reverse/right reads of reference"
rliterman@0 71 @echo "\t\t\t [default='_2.fastq.gz']"
rliterman@0 72 @echo " --ref_forward=STR\tFull file extension for forward/left reads of reference"
rliterman@0 73 @echo "\t\t\t [default='_1.fastq.gz']"
rliterman@0 74 @echo " --ref_reverse=STR\tFull file extension for reverse/right reads of reference"
rliterman@0 75 @echo "\t\t\t [default='_2.fastq.gz']"
rliterman@0 76 @echo " --readext=STR\t\tExtension for single-end reads for query [default='fastq.gz']"
rliterman@0 77 @echo " --ref_readext=STR\tExtension for single-end reads for reference"
rliterman@0 78 @echo "\t\t\t [default='fastq.gz']"
rliterman@0 79 @echo " --min_cov=NUM\t\tDo not analyze queries that cover less than <min_cov>% of the"
rliterman@0 80 @echo "\t\t\treference assembly [default=85]"
rliterman@0 81 @echo " --min_iden=NUM\tOnly consider alignments where the percent identity is at least"
rliterman@0 82 @echo "\t\t\t <min_iden> [default=99]"
rliterman@0 83 @echo " --min_len=NUM\t\tOnly consider alignments that span at least <min_len> in bp"
rliterman@0 84 @echo "\t\t\t [default=500]"
rliterman@0 85 @echo " --dwin=LIST\t\tA comma-separated list of windows to check SNP densities"
rliterman@0 86 @echo "\t\t\t [default=1000,125,15]"
rliterman@0 87 @echo " --wsnps=LIST\t\tThe maximum number of SNPs allowed in the corresponding window from"
rliterman@0 88 @echo "\t\t\t --dwin [default=3,2,1]"
rliterman@0 89 @echo " --query_edge=NUM\tOnly consider SNPs that occur within <query_edge>bp of the end"
rliterman@0 90 @echo "\t\t\t of a query contig [default=250]"
rliterman@0 91 @echo " --ref_edge=NUM\tOnly consider SNPs that occur within <query_edge>bp of the end"
rliterman@0 92 @echo "\t\t\t of a reference contig [default=250]"
rliterman@0 93 @echo " --n_ref=NUM\t\tThe number of RefChooser reference isolates to consider (only"
rliterman@0 94 @echo "\t\t\t applied if using RefChooser) [default=3]"
rliterman@0 95 @echo " --reads=PATH\t\tLocation of query read data (Path to directory, or path to file with"
rliterman@0 96 @echo "\t\t\t multiple directories)"
rliterman@0 97 @echo " --fasta=PATH\t\tLocation of query assembly data (Path to directory containing"
rliterman@0 98 @echo "\t\t\t FASTAs, path to FASTA, path to multiple FASTAs)"
rliterman@0 99 @echo " --ref_reads=PATH\tLocation of reference read data (Path to directory, or path to"
rliterman@0 100 @echo "\t\t\t file with multiple directories)"
rliterman@0 101 @echo " --ref_fasta=PATH\tLocation of reference assembly data (Path to directory"
rliterman@0 102 @echo "\t\t\t containing FASTAs, path to FASTA, path to multiple FASTAs)"
rliterman@0 103 @echo " --trim_name=STR\tA string in assembly file names that you want to remove from"
rliterman@0 104 @echo "\t\t\t sample IDs (e.g., _contigs_skesa)"
rliterman@0 105
rliterman@0 106 config:
rliterman@0 107 @cat <<- EOF
rliterman@0 108 profiles {
rliterman@0 109 standard {
rliterman@0 110 process.executor = 'local'
rliterman@0 111 params.cores = `nproc --all`
rliterman@0 112 }
rliterman@0 113 }
rliterman@0 114 EOF > ~/.nextflow/config
rliterman@0 115
rliterman@0 116
rliterman@0 117 ifeq (screen, $(firstword $(MAKECMDGOALS)))
rliterman@0 118 runargs := $(wordlist 2, $(words $(MAKECMDGOALS)), $(MAKECMDGOALS))
rliterman@0 119 $(eval $(runargs):;@true)
rliterman@0 120 endif
rliterman@0 121
rliterman@0 122 ifeq (snp, $(firstword $(MAKECMDGOALS)))
rliterman@0 123 runargs := $(wordlist 2, $(words $(MAKECMDGOALS)), $(MAKECMDGOALS))
rliterman@0 124 $(eval $(runargs):;@true)
rliterman@0 125 endif
rliterman@0 126
rliterman@0 127 screen: config ## determine whether query isolates are close to a reference
rliterman@0 128 nextflow run CSP2.nf -profile standard --runmode screen $(runargs)
rliterman@0 129
rliterman@0 130 snp: config ## generate pairwise distances for a set of query isolates
rliterman@0 131 nextflow run CSP2.nf -profile standard --runmode snp $(runargs)
rliterman@0 132
rliterman@0 133 snpdiffs: config
rliterman@0 134
rliterman@0 135 test_screen:
rliterman@0 136 nextflow run CSP2.nf -profile standard --runmode screen --fasta assets/Screen/Assembly/Week_42_Assembly.fasta --reads assets/Screen/Reads/ --ref_fasta assets/Screen/Assembly/Lab_Control.fasta --out ./CSP2_Test_Screen --readext fq.gz --forward _1.fq.gz --reverse _2.fq.gz
rliterman@0 137
rliterman@0 138 test_snp:
rliterman@0 139 nextflow run CSP2.nf -profile standard --runmode snp --fasta assets/SNP/ --n_ref 3 --out ./CSP2_Test_SNP --max_missing 50
rliterman@0 140
rliterman@0 141 test: config test_screen test_snp
rliterman@0 142 ls -lah assets/Screen/Output/Contamination_Screen/
rliterman@0 143 diff -bur ./CSP2_Test_SNP/snpdiffs assets/SNP/Output/Soil_Analysis/snpdiffs