Merge pull request #40 from karinlag/master

Closing issue 38

LICENSE

@@ -23,4 +23,4 @@ OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
 HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
 LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
 OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGE.
+SUCH DAMAGE.

asm_annot.nf

@@ -25,12 +25,6 @@ log.info "Results can be found in : ${params.out_dir}"
 log.info "================================================="
 log.info ""
 
-// Needed to run on the Abel cluster
-preCmd = """
-if [ -f /cluster/bin/jobsetup ];
-then set +u; source /cluster/bin/jobsetup; set -u; fi
-"""
-
 // First, define the input data that go into input channels
 Channel
     .fromFilePairs( params.reads, size:params.setsize )
@@ -50,7 +44,6 @@ process run_fastqc {
     file "$pair_id" into fastqc_results
 
     """
-    ${preCmd}
     mkdir ${pair_id}
     fastqc -q ${reads} -o ${pair_id} -t $task.cpus
     """
@@ -68,7 +61,6 @@ process run_multiqc {
     file "multiqc_report.html" into multiqc_report
 
     """
-    ${preCmd}
     multiqc fastqc_output
     """
 }
@@ -88,7 +80,6 @@ process collate_data {
     set pair_id, file("${pair_id}*_concat.fq.gz") into (reads, pilon_reads)
 
     """
-    ${preCmd}
     cat ${pair_id}*R1* > ${pair_id}_R1_concat.fq.gz
     cat ${pair_id}*R2* > ${pair_id}_R2_concat.fq.gz
     """
@@ -111,7 +102,6 @@ process run_strip {
     file "${pair_id}_bbduk_output.log"
 
     """
-    ${preCmd}
     bbduk.sh threads=$task.cpus ref=${params.stripgenome} \
     in1=${pair_id}_R1_concat.fq.gz \
     in2=${pair_id}_R2_concat.fq.gz \
@@ -138,7 +128,6 @@ process run_trim {
     file "${pair_id}_concat_stripped_trimmed.log"
 
     """
-    ${preCmd}
     trimmomatic PE -threads $task.cpus -trimlog ${pair_id}_concat_stripped_trimmed.log ${pair_id}*_concat_stripped.fq.gz \
     -baseout ${pair_id}_trimmed.fq.gz ILLUMINACLIP:${params.adapter_dir}/${params.adapters}:${params.illuminaClipOptions} \
     SLIDINGWINDOW:${params.slidingwindow} \
@@ -169,7 +158,6 @@ process run_spadesasm {
      file "${pair_id}_spades.log"
 
      """
-     ${preCmd}
      spades.py ${params.careful} --cov-cutoff=${params.cov_cutoff} \
      -1 ${pair_id}_R1_concat_stripped_trimmed.fq.gz \
      -2 ${pair_id}_R2_concat_stripped_trimmed.fq.gz \
@@ -202,7 +190,6 @@ process run_bwamem {
      file("${pair_id}_mapped_sorted.bam.bai") into bwamem_results
 
      """
-     ${preCmd}
      bwa index ${pair_id}_spades_scaffolds_min${params.min_contig_len}.fasta
      bwa mem -t $task.cpus  ${pair_id}_spades_scaffolds_min${params.min_contig_len}.fasta \
      *.fq.gz | samtools sort -o ${pair_id}_mapped_sorted.bam -
@@ -230,7 +217,6 @@ process run_pilon {
     file "${pair_id}_pilon_spades.fasta" into asms_for_quast
 
     """
-    ${preCmd}
     export _JAVA_OPTIONS=$task.javaopts
     pilon --threads $task.cpus --genome ${pair_id}_spades_scaffolds_min${params.min_contig_len}.fasta \
     --bam ${pair_id}_mapped_sorted.bam --output ${pair_id}_pilon_spades \
@@ -252,7 +238,6 @@ process run_prokka {
     set pair_id, file("${pair_id}.*") into annotation_results
 
     """
-    ${preCmd}
     prokka --compliant --force --usegenus --cpus $task.cpus \
     --centre ${params.centre} --prefix ${pair_id} --locustag ${params.locustag} \
     --genus ${params.genus} --species ${params.species} \
@@ -278,9 +263,7 @@ process quast_eval {
     file quast_evaluation_all into quast_evaluation_all
 
     """
-    ${preCmd}
     quast --threads $task.cpus -o quast_evaluation_all \
-    -G ${params.quast_genes} -R ${params.quast_ref} \
-    --scaffolds ${asm_list}
+    -g ${params.quast_genes} -R ${params.quast_ref} ${asm_list}
     """
 }

bin/filetypes.py

@@ -26,5 +26,3 @@ def lane(filename):
             if field.startswith("L00"):
                 lane = field
         return lane
-
-

conf/asm_annot_template.config

@@ -25,8 +25,8 @@ params.help = false
 params.savemode = "copy"
 
 // BBDuk params, has to be absolute paths
-params.stripgenome = "/work/projects/nn9305k/genome_references/genomes/PhiX/PhiX.fasta"
-params.stripdir = "/work/projects/nn9305k/genome_references/bbmap_refs"
+params.stripgenome = "/cluster/projects/nn9305k/genome_references/genomes/PhiX/PhiX.fasta"
+params.stripdir = "/cluster/projects/nn9305k/genome_references/bbmap_refs"
 
 
 // Trimmomatic configuration variables
@@ -37,7 +37,7 @@ params.leading = 3
 params.trailing = 3
 params.minlen = 36
 params.adapters = "TruSeq3-PE.fa"
-params.adapter_dir = "/home/karinlag/bin/Trimmomatic-0.36/adapters"
+params.adapter_dir = "/cluster/projects/nn9305k/db_flatfiles/trimmomatic_adapters"
 
 
 // SPAdes configuration variables
@@ -58,6 +58,6 @@ params.centre = "NVI"
 
 
 // QUAST variables
-params.genome_directory = "/work/projects/nn9305k/genome_references/genomes/"
+params.genome_directory = "/cluster/projects/nn9305k/genome_references/genomes/"
 params.quast_ref = "${params.genome_directory}ecoli/GCF_000005845.2_ASM584v2_genomic.fna"
 params.quast_genes = "${params.genome_directory}ecoli/GCF_000005845.2_ASM584v2_genomic.gff"

conf/condaslurm.config

@@ -5,5 +5,5 @@
 */
 
 process {
-  conda = '/work/projects/nn9305k/src/anaconda3/envs/bifrost'
+  conda = '/cluster/projects/nn9305k/src/miniconda/envs/bifrost'
 }

conf/condastandard.config

@@ -6,5 +6,5 @@
 */
 
 process {
-  conda = '/home/karinlag/anaconda3/envs/bifrost'
+  conda = '/home/karinlag/src/anaconda3/envs/bifrost'
 }

conf/qc_track_template.config

@@ -21,7 +21,7 @@ params.out_dir = "track_one"
 // General configuration variables
 params.pwd = "$PWD"
 params.help = false
-params.savemode = "link"
+params.savemode = "copy"
 
 // Raw fastqc results
 params.fastqc = "fastqc"

conf/slurm.config

@@ -19,12 +19,12 @@
 
 process {
     executor = 'slurm'
-    clusterOptions = '--job-name=nxf_test --account=nn9305k --mem-per-cpu=3140'
+    clusterOptions = '--job-name=nxf_test --account=nn9305k --mem-per-cpu=4700M'
     queueSize = 24
     maxRetries = 3
     errorStrategy='retry'
 
-    cpus = 16
+    cpus = 20
     withLabel: one {cpus = 1}
 
     //this is mostly for pilon, but can be used elsewhere too

conf/third_party_software.md

@@ -1,11 +1,11 @@
 # Third party software
 
-The Bifrost pipeline depends on several third party packages. 
+The Bifrost pipeline depends on several third party packages.
 These have to be made available to the pipeline in some way.
 The way that these are made available to the pipeline depends
 on which system the pipeline is being run on.
 
-Please note: not all of the software is used for all tracks. 
+Please note: not all of the software is used for all tracks.
 The track(s) that each software is used in is noted below.
 
 
@@ -27,7 +27,7 @@ There are currently three tracks:
 * Track Three: Trimming with trimmomatic followed by assembly
     with SPAdes. Trimming results are evaluated with MultiQC, and
     assemblies with QUAST
-    
+
 ## Profiles
 
 We currently have two profiles set up, standard and slurm.
@@ -36,16 +36,11 @@ We currently have two profiles set up, standard and slurm.
 This profile is used when running on a normal stand-alone
 computer. This assumes that all software is available on
 the command line, unless otherwise noted with a full path in
-the standard.config file. 
+the standard.config file.
 
 ### slurm.config
 This profile is used when running on a system that uses the
 slurm queue management system. At present, this also depends
 heavily on the module system. Any software not in the module
-system needs to either be available on the command line, or 
-should be specified using the full path. 
-
-
-
-
-
+system needs to either be available on the command line, or
+should be specified using the full path.

qc_track.nf

@@ -22,12 +22,6 @@ log.info "Results can be found in : ${params.out_dir}"
 log.info "================================================="
 log.info ""
 
-// Needed to run on the Abel cluster
-preCmd = """
-if [ -f /cluster/bin/jobsetup ];
-then set +u; source /cluster/bin/jobsetup; set -u; fi
-"""
-
 // First, define the input data that go into input channels
 Channel
     .fromFilePairs( params.reads, size:params.setsize )
@@ -48,7 +42,6 @@ process run_fastqc {
     file "$pair_id" into fastqc_results
 
     """
-    ${preCmd}
     mkdir ${pair_id}
     fastqc -q ${reads} -o ${pair_id} -t $task.cpus
     """
@@ -66,7 +59,6 @@ process run_multiqc {
     file "multiqc_report.html" into multiqc_report
 
     """
-    ${preCmd}
     multiqc fastqc_output
     """
 }

specific_genes.nf

@@ -24,11 +24,6 @@ log.info "Results can be found in : ${params.out_dir}"
 log.info "================================================="
 log.info ""
 
-preCmd = """
-if [ -f /cluster/bin/jobsetup ];
-then set +u; source /cluster/bin/jobsetup; set -u; fi
-"""
-
 // First, define the input data that go into input channels
 Channel
     .fromFilePairs( params.reads, size:params.setsize )
@@ -55,7 +50,6 @@ process collate_data {
       (read_pairs_mlst, read_pairs_amr, read_pairs_vir)
 
     """
-    ${preCmd}
     cat ${pair_id}*R1* > ${pair_id}_R1_concat.fq.gz
     cat ${pair_id}*R2* > ${pair_id}_R2_concat.fq.gz
     """
@@ -77,7 +71,6 @@ process run_ariba_mlst_prep {
     params.do_mlst == "yes"
 
     """
-    ${preCmd}
     ariba pubmlstget "${params.mlst_scheme}" mlst_db
     """
 }
@@ -100,7 +93,6 @@ process run_ariba_mlst_pred {
     params.do_mlst == "yes"
 
     """
-    ${preCmd}
     ariba run --threads $task.cpus mlst_db/ref_db ${pair_id}_R*_concat.fq.gz ${pair_id}_ariba &> ariba.out
     echo -e "header\t" \$(head -1 ${pair_id}_ariba/mlst_report.tsv) > ${pair_id}_mlst_report.tsv
     echo -e "${pair_id}\t" \$(tail -1 ${pair_id}_ariba/mlst_report.tsv) >> ${pair_id}_mlst_report.tsv
@@ -123,7 +115,6 @@ process run_ariba_mlst_summarize {
     params.do_mlst == "yes"
 
     """
-    ${preCmd}
     cat ${pair_id_mlst_tsv} >> mlst_summarized_results_tmp.tsv
     head -1 mlst_summarized_results_tmp.tsv > mlst_summarized_results.tsv
     cat mlst_summarized_results_tmp.tsv | grep -v "ST" >> mlst_summarized_results.tsv
@@ -145,7 +136,6 @@ process run_ariba_amr_prep {
     params.do_amr == "yes"
 
     """
-    ${preCmd}
     ariba getref ${params.amr_db} amr_db
     ariba prepareref -f amr_db.fa -m amr_db.tsv db_amr_prepareref
     """
@@ -168,7 +158,6 @@ process run_ariba_amr_pred {
 
 
     """
-    ${preCmd}
     ariba run --threads $task.cpus db_amr_prepareref ${pair_id}_R*_concat.fq.gz ${pair_id}_ariba &> ariba.out
     cp ${pair_id}_ariba/report.tsv ${pair_id}_amr_report.tsv
 
@@ -191,7 +180,6 @@ process run_ariba_amr_summarize {
     params.do_amr == "yes"
 
     """
-    ${preCmd}
     ariba summary amr_summarized ${pair_id_amr_tsv}
     """
 }
@@ -209,7 +197,6 @@ process run_ariba_vir_prep {
     params.do_vir == "yes"
 
     """
-    ${preCmd}
     ariba getref ${params.vir_db} vir_db
     ariba prepareref -f vir_db.fa -m vir_db.tsv db_vir_prepareref
     """
@@ -231,7 +218,6 @@ process run_ariba_vir_pred {
     params.do_vir == "yes"
 
     """
-    ${preCmd}
     ariba run --threads $task.cpus db_vir_prepareref ${pair_id}_R*_concat.fq.gz \
       ${pair_id}_ariba &> ariba.out
     cp ${pair_id}_ariba/report.tsv ${pair_id}_vir_report.tsv
@@ -255,7 +241,6 @@ process run_ariba_vir_summarize {
     params.do_vir == "yes"
 
     """
-    ${preCmd}
     ariba summary vir_summarized ${pair_id_vir_tsv}
     """
 }