update singularity / apptainer image

fix version in binning.sif instead require minimal version and install new version of binette with conda

changed milestone to %Issues en vrac

added Enhancement label

changed milestone to %Add MetaMDBG

Certains outils sont sur des versions anciennes dans l'image singularity.

• cutadapt 4.2 -> 4.9
• diamond 2.0.15 -> 2.1.8.162
• diamond 2.0.15 -> 2.1.12
• fastqc 0.11.9 -> 0.12.1
• flye 2.9.1 -> 2.9.4
• kaiju 1.9.2 -> 1.10.1
• minimap2 2.24 -> 2.28
• multiqc 1.14 -> 1.23
• samtools 1.15.1 -> 1.20
• spades 3.15.5 -> 4.0.0
• gtdbtk 2.1 -> 2.4

-> envisager une mise à jour + tests avant nouvelle version du pipeline ?

mentioned in issue #251 (closed)

assigned to @philipperuiz

Process nf ayant une seule dépendance (et donc pouvant etre facilement upgradé)

ETAPE / MODULE	PROCESS	script	version	derniere version en ligne	ETAT (TODO/NOT UPGRADABLE/DONE)
Assembly	METAFLYE	flye	2.9.1	2.9.5	[ ]
	HIFIASM_META	hifiasm_meta	hamtv0.3
	MEGAHIT	megahit	1.2.9	1.2.9
	METASPADES	metaspades.py	spades=3.15.5	4.0.0
binning	METABAT2	metabat2	2.15	2.17
	MAXBIN2	run_MaxBin.pl	2.2.7	2.2.7
	CONCOCT	several script	1.1.0	1.1.0	up to date, n'a pas bougé depuis 2019
modules seuls
	BARRNAP	barrnap	0.9	0.9
	CHECKM2	checkm2	utilise celui de binette (v1.*)	1.0.2
	CUTADAPT	cutadapt	4.2	5.0	DONE CN / testé validé test functionnel
	DIAMOND	diamond+unix command	2.0.15	2.1.11
	DREP	dRep + retrieve_bins_cluster_composition	3.0.0	3.4.2	NOT UPGRADABLE
	EGGNOG_MAPPER	emapper.py	2.1.9	2.1.12	TODO
	FASTQC	fastqc	0.11.9	0.12.1	testé validé test functionnel
	FEATURE_COUNTS	featureCounts	subread=2.0.3	2.0.8
	GTDBTK	gtdbtk	2.1	2.4	testé validé partiel test functionnel + mash_db (get_db_version non fonctionnel pour mash si n'existe pas au départ)
	HOST_FILTER	bwa-mem2,samtools	2.2.1 & 1.15.1	2.2.1 & 1.21
	HOST_FILTER_HIFI	minimap2,samtools	2.24, 1.15.1	2.28 & 1.21
	KAIJU	kaiju,kaiju2krona, kaiju2table	1.9.2	1.10.1	TODO PR
	KAIJU_TO_KRONA	ktImportText	krona=2.8.1	2.8.1
	PLOT_KRONA	ktImportText	krona=2.8.1	2.8.1
	QUAST	metaquast.py	quast=5.2.0	5.3.0
	MULTIQC	multiqc	1.14	1.27	testé validé test functionnel
	PRODIGAL	prodigal	2.6.3	2.6.3
	GET_ALIGNMENT_METRICS	samtools	1.15.1	1.21
	BWA_MEM	bwa-mem2 & samtools	2.2.1 & 1.15.1	2.2.1 & 1.21	TODO samtools a essayer
	MINIMAP2	minimap2 & samtools	2.24, 1.15.1	2.28 & 1.21
	READS_DEDUPLICATION	bwa-mem2 & samtools	2.2.1 & 1.15.1	2.2.1 & 1.21
	SICKLE	sickle	sickle-trim=1.33	1.33
	TRNASCAN_SE	tRNAscan-SE	2.0.11	2.0.12

Voici un exemple de configuration pour mettre a jour GTDBTK :

process {
	withName:GTDBTK {
                container = 'quay.io/biocontainers/gtdbtk:2.4.0--pyhdfd78af_2'
		memory = { 150.GB }
		cpus = 2 
           }
}

created branch 242-update-singularity-apptainer-image to address this issue

Dépendances Python de l'image binning.sif v2.4.3 (téléchargée via le lien de la documentation)

library	version	derniere version en ligne	script	ETAT (TODO/NOT UPGRADABLE/DONE)
free
pandas	1.5.3	2.2.3	multiple .py functions
scipy	1.10.1	1.15.1	plot_kaiju_stas.py
setuptools	65.6.3	75.8.0	?
requests	2.28.1	2.32.3	?
packaging	23.0	24.1	?
tqdm	4.65	4.67.1	?
networkx	2.8.4	3.4.2	?
pyfastx	1.0.1	2.2.0	multiple .py functions
pyrodigal	2.1.0	3.6.3	?
matplotlib	3.7.1	3.9.0	aln_to_tax_affi.py
pprodigal	1.0.1	?	?

mentioned in merge request !27 (merged)

mentioned in commit 0a77b6c6

mentioned in commit d20c1b2e

mentioned in merge request !29 (merged)

mentioned in commit 7a02981b

mentioned in merge request !30 (merged)

mentioned in commit 036fa288

• test.config modifier -> ok

marked this issue as related to #263

marked this issue as related to #260