Hmmsearch

#!/user/bin/nextflow
nextflow.enable.dsl=2


/// INPUTS
DIR_input = "/mnt/scgc_nfs/lab/ggavelis/sandbox/nf_tests/hmmer"
SUFFIX_of_input_files = ".faa"

// OUTPUT
DIR_output = "results"

///  HMM to search against
PATH_hmm = "/mnt/scgc_nfs/ref/kofamscan/profiles/K19868.hmm"



/// DEV MODE STUFF
params.dev = false // Lets user testrun nextflow command (by adding flag '--dev') which will have this pipeline run on JUST ONE SAG (again, as a test)
params.num_inputs = 2


workflow {
	CH_sample_id_AND_faa = channel
		.fromPath("$DIR_input/*$SUFFIX_of_input_files", checkIfExists:true) // --> path(faa)
		.map { it -> tuple(it.getBaseName(), it) } // --> tuple( val(sample_id), path(faa))    #  1. Extracts sample_id using .getBaseName(), then stores it in a tuple (with the inputfile path)
		//.view()
	HMMER_v3_3_2( CH_sample_id_AND_faa.take( params.dev ? params.num_inputs : -1) ) //.take(params.dev ? params.num_inputs : -1)
}

process HMMER_v3_3_2 {
	container='docker://quay.io/biocontainers/hmmer:3.3.2--h87f3376_2'
	publishDir DIR_output
	cpu=2
	tag "${sample_id}"

	input: tuple val(sample_id), path(faa)

	output: tuple val(sample_id), path("${sample_id}_hmm_tbl.txt")

	"hmmsearch -E 0.00001 --tblout ${sample_id}_hmm_tbl.txt ${PATH_hmm} ${faa} &> /dev/null"
}