From e0ede9ef59f11f42a4a5d1343da150720c22ec50 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 4 Oct 2024 17:21:18 +0100
Subject: [PATCH] added test correction tmtplex

---
 .github/workflows/ci.yml  |  2 +-
 conf/test_tmt_corr.config | 35 +++++++++++++++++++++++++++++++++++
 2 files changed, 36 insertions(+), 1 deletion(-)
 create mode 100644 conf/test_tmt_corr.config

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 02d3d605..8819f896 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -34,7 +34,7 @@ jobs:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
-        test_profile: ["test_lfq", "test_lfq_sage", "test_dia", "test_localize", "test_tmt", "test_dda_id"]
+        test_profile: ["test_lfq", "test_lfq_sage", "test_dia", "test_localize", "test_tmt", "test_dda_id", "test_tmt_corr"]
         exec_profile: ["docker"]
         exclude:
           - test_profile: test_dia
diff --git a/conf/test_tmt_corr.config b/conf/test_tmt_corr.config
new file mode 100644
index 00000000..561d1f31
--- /dev/null
+++ b/conf/test_tmt_corr.config
@@ -0,0 +1,35 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running full-size tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a full size pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test_tmt,<docker/singularity> [--outdir <OUTDIR>]
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Full test profile DDA ISO'
+    config_profile_description = 'Full test dataset in isotopic labelling mode to check pipeline function and sanity of results'
+
+    outdir = "./results_iso"
+
+    max_cpus = 2
+    max_memory = 6.GB
+    max_time = 48.h
+
+    // Input data for full size test
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/PXD000001.sdrf.tsv'
+
+    database = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/erwinia_carotovora.fasta'
+    posterior_probabilities = "percolator"
+    search_engines = "comet,msgf"
+    psm_level_fdr_cutoff = 1.0
+    decoy_string = "rev"
+    add_decoys = true
+    protocol = 'TMT'
+    isotope_correction = true
+    plex_corr_matrix_file = 'assets/tmt6plex_default_correction.matrix'
+}