add Docker,nf

Dockerfile

+##### BASE #####
+FROM python:3.10-slim-buster
+
+##### VARIABLES #####
+WORKDIR /Users/terminal-fragment-selector
+
+COPY requirements.txt /Users/terminal-fragment-selector/requirements.txt
+COPY requirements_dev.txt /Users/terminal-fragment-selector/requirements_dev.txt
+
+##### INSTALL #####
+RUN pip install -r /Users/terminal-fragment-selector/requirements.txt
+RUN pip install -r /Users/terminal-fragment-selector/requirements_dev.txt
+
+
+
+

frag_selec.nf

+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+```c
+/*   
+ * Define the input parameters"""Takes as input FASTA file
+                                     of cDNA sequences, a CSV/TSV with sequence
+                                     counts, and mean and std. dev. of fragment
+                                     lengths and 4 nucleotide probabilities
+                                     for the cuts. Outputs most terminal
+                                     fragment (within desired length range)
+                                     for each sequence."""
+ */ 
+params.fasta_file = "$projectDir/tests/test_files/test,fasta"
+params.counts_file = "$projectDir/tests/test_files/test.csv"        
+params.sep = "$projectDir/data/yeast/sep/sep.csv"
+params.outdir = "results" 
+
+
+/* Log some information for the user */
+
+log.info """\
+         R N A S E Q - N F   P I P E L I N E 
+         ===================================       
+         fasta_file   : ${params.fasta_file}      
+         counts_file  : ${params.counts_file}             
+         outdir       : ${params.outdir}          
+         """                                        
+         .stripIndent() 
+         
+/* 
+ * Define the `file_validation` process:
+ * Validate input files exist and are the correct format
+ */ 
+
+process file_validation { 
+
+    input:
+    path fasta_file
+    path counts_file
+    path sep 
+    
+    output:
+    tuple: fasta dict and sequence for counts file
+    
+    script: 
+    """
+    salmon index --threads $task.cpus -t $transcriptome -i index
+    """ 
+}    
+    
+
+/*
+ * Define the get_cut_number process:
+ * Get the number of cuts for a particular sequence 
+ */
+
+process get_cut_number {
+
+    tag "get_cut_numbern on $n_cuts" 
+    publishDir "${params.outdir}/get_cut_number", mode:'copy' 
+    
+    input:
+    path index
+    tuple val(n_cuts), path(seq_len, mean)                                                                                   
+    
+    output:
+    path(n_cuts)
+    
+    script:
+    """
+      
+    """                                                      
+}
+
+
+/* 
+ * Define the fragmentation process:
+ * Fragment cDNA sequences and select terminal fragment 
+ */
+
+process fragmentation {
+
+    tag "fragmentation on $fasta, seq_counts, nuc_probs, mu_length, std"
+    
+    input:
+    dict val(fasta), pd.DataFrame(seq_counts), dict(nuc_probs),int(mu_length),int(std)
+    
+    output:
+    path("term_frags")
+    
+    script:
+    """
+    mkdir fastqc_${sample_id}_logs
+    
+    """
+}
+
+
+
+/* Start the job:
+ * initialize variables
+ */
+ 
+Channel
+    .fromFilePairs( params.reads, checkIfExists:true ) 
+    .set { read_pairs_ch }     
+
+
+/* The "main" function:
+ * Use CLI arguments to fragment sequences and output text file with selected terminal fragments
+ */
+
+workflow {
+  file_validation_ch=file_validation(params.fasta_file, params.counts_file, params.sep)
+  get_cut_number_ch = get_cut_number(seq_len, mean)
+  framentation_ch = fregmentation(fasta, seq_counts, nuc_probs, mu_length, std)                                                                           }                                                                                                                     
+
+
+/* Book keeping upon workflow completion */
+workflow.onComplete {
+   log.info (workflow.success ? "\nDone! Open the following report in your browser -->     $params.outdir/multiqc/multiqc_report.html\n" : "Oops .. something went wrong") 
+   )
+}                                                                                                                     
+```

requirements.txt

 argparse
-biopython >= 1.78
+biopython
 numpy >= 1.23.3
 pandas >= 1.4.4
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