From df05b47ed3e8d9c3788fd02841165c422ccc83ff Mon Sep 17 00:00:00 2001
From: Mate Balajti <mate.balajti@unibas.ch>
Date: Mon, 18 Sep 2023 12:12:52 +0000
Subject: [PATCH] refactor: minor updates
---
.gitlab-ci.yml | 2 +-
Dockerfile | 18 -------
frag_selec.nf | 126 ---------------------------------------------
setup.py | 2 +-
tests/test_frag.py | 4 +-
5 files changed, 4 insertions(+), 148 deletions(-)
delete mode 100644 Dockerfile
delete mode 100644 frag_selec.nf
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0ab9bf0..0c14af8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -31,4 +31,4 @@ lint-test-job: # This job also runs in the test stage.
- pip install -e .
- flake8 --docstring-convention google term_frag_sel/ tests/
- pylint term_frag_sel/ tests/
- - mypy term_frag_sel/
+ - mypy term_frag_sel/ tests/
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index 4ca5d5f..0000000
--- a/Dockerfile
+++ /dev/null
@@ -1,18 +0,0 @@
-##### 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 apt-get update \
-&& apt-get install gcc -y \
-&& apt-get clean
-RUN pip install -r requirements.txt -r requirements_dev.txt
-
-
-
-
diff --git a/frag_selec.nf b/frag_selec.nf
deleted file mode 100644
index 1fc9bdc..0000000
--- a/frag_selec.nf
+++ /dev/null
@@ -1,126 +0,0 @@
-#!/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")
- )
-}
-```
diff --git a/setup.py b/setup.py
index 3fe12de..469d786 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,6 @@
"""Set up project."""
from pathlib import Path
-from setuptools import setup, find_packages
+from setuptools import setup, find_packages # type: ignore
project_root_dir = Path(__file__).parent.resolve()
with open(project_root_dir / "requirements.txt",
diff --git a/tests/test_frag.py b/tests/test_frag.py
index da2d5bb..90c0f94 100644
--- a/tests/test_frag.py
+++ b/tests/test_frag.py
@@ -1,7 +1,7 @@
"""Test utils.py functions."""
-import pandas as pd
+import pandas as pd # type: ignore
import pytest
-from Bio import SeqIO
+from Bio import SeqIO # type: ignore
from term_frag_sel.fragmentation import fragmentation
--
GitLab