Merge pull request #345 from BU-ISCIII/develop

Develop merge for 2.2.1 release

CHANGELOG.md

@@ -44,6 +44,36 @@ Code contributions to the hotfix:
 
 ### Requirements
 
+## [2.2.1] - 2024-10-01 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.1
+
+### Credits
+
+Code contributions to the new version:
+
+- [Daniel Valle](https://github.com/Daniel-VM)
+- [Sarai Varona](https://github.com/svarona)
+- [Victor Lopez](https://github.com/victor5lm)
+- [Sergio Olmos](https://github.com/OPSergio)
+
+### Template fixes and updates
+
+- Fixed path to blast database and update Emmtyper params [#339](https://github.com/BU-ISCIII/buisciii-tools/pull/339)
+- Updated sarek version (v3.4.4) in ExomeEB-ExomeTrio-WGSTrio templates [#341] (https://github.com/BU-ISCIII/buisciii-tools/pull/341)
+- Fixed IRMAs config for amended consensus [#325](https://github.com/BU-ISCIII/buisciii-tools/pull/325).
+- Improved excel_generator.py and bioinfo_doc.py email creation function, and updated sftp_user.json, setup.py, main.py and some lablogs [#344](https://github.com/BU-ISCIII/buisciii-tools/pull/344).
+
+### Modules
+
+#### Added enhancements
+
+#### Fixes
+
+#### Changed
+
+#### Removed
+
+### Requirements
+
 ## [2.2.0] - 2024-09-12 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.0
 
 ### Credits

bu_isciii/__main__.py

@@ -57,7 +57,7 @@ def run_bu_isciii():
     )
 
     # stderr.print("[green]                                          `._,._,'\n", highlight=False)
-    __version__ = "2.2.0"
+    __version__ = "2.2.1"
     stderr.print(
         "[grey39]    BU-ISCIII-tools version {}".format(__version__), highlight=False
     )

bu_isciii/bioinfo_doc.py

@@ -646,10 +646,43 @@ def email_creation(self):
                     email_data["email_notes"] = self.delivery_notes.replace(
                         "\n", "<br />"
                     )
+                else:
+                    email_data["email_notes"] = bu_isciii.utils.ask_for_some_text(
+                        msg="Write email notes"
+                    ).replace("\n", "<br />")
             else:
-                email_data["email_notes"] = bu_isciii.utils.ask_for_some_text(
-                    msg="Write email notes"
-                ).replace("\n", "<br />")
+                if bu_isciii.utils.prompt_yn_question(
+                    msg="Do you wish to provide a text file for email notes?",
+                    dflt=False,
+                ):
+                    for i in range(3, -1, -1):
+                        email_data["email_notes"] = bu_isciii.utils.prompt_path(
+                            msg="Write the path to the file with RAW text as email notes"
+                        )
+                        if not os.path.isfile(
+                            os.path.expanduser(email_data["email_notes"])
+                        ):
+                            stderr.print(
+                                f"Provided file doesn't exist. Attempts left: {i}"
+                            )
+                        else:
+                            stderr.print(f"File selected: {email_data['email_notes']}")
+                            break
+                    else:
+                        stderr.print(
+                            "No more attempts. Email notes will be given by prompt"
+                        )
+                        email_data["email_notes"] = None
+                else:
+                    email_data["email_notes"] = None
+
+                if email_data["email_notes"]:
+                    with open(os.path.expanduser(email_data["email_notes"])) as f:
+                        email_data["email_notes"] = f.read().replace("\n", "<br />")
+                else:
+                    email_data["email_notes"] = bu_isciii.utils.ask_for_some_text(
+                        msg="Write email notes"
+                    ).replace("\n", "<br />")
 
         email_data["user_data"] = self.resolution_info["service_user_id"]
         email_data["service_id"] = self.service_name.split("_", 5)[0]

bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog

@@ -9,31 +9,6 @@ cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --cpu
 
 echo 'bash create_irma_stats.sh' > _02_create_stats.sh
 
-echo "ls */*HA*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | sort -u | cut -d '_' -f3  | sed '/^\$/d' | sed 's/^/A_/g' > HA_types.txt" > _03_post_processing.sh
+echo 'bash postprocessing.sh' > _03_post_processing.sh
 
-echo 'cat HA_types.txt | while read type; do if test -d ${type}; then rm -rf ${type}; fi; done; if test -d B ; then rm -rf B; fi; if test -d C; then rm -rf C; fi' >> _03_post_processing.sh
-
-echo 'if test -f all_samples_completo.txt; then rm all_samples_completo.txt; fi' >> _03_post_processing.sh
-
-echo "cat HA_types.txt | while read in; do mkdir \${in}; done" >> _03_post_processing.sh
-
-echo "if grep -qw 'B__' irma_stats.txt; then mkdir B; fi" >> _03_post_processing.sh
-
-echo "if grep -qw 'C__' irma_stats.txt; then mkdir C; fi" >> _03_post_processing.sh
-
-echo "ls */*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | cut -d '_' -f1,2 | sort -u | grep 'A_' > A_fragment_list.txt" >> _03_post_processing.sh
-
-echo "ls */*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | cut -d '_' -f1,2 | sort -u | grep 'B_' > B_fragment_list.txt" >> _03_post_processing.sh
-
-echo "ls */*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | cut -d '_' -f1,2 | sort -u | grep 'C_' > C_fragment_list.txt" >> _03_post_processing.sh
-
-echo 'cat HA_types.txt | while read type; do grep ${type} irma_stats.txt | cut -f1 | while read sample; do cat A_fragment_list.txt | while read fragment; do if test -f ${sample}/${fragment}*.fasta; then cat ${sample}/${fragment}*.fasta | sed "s/^>/\>${sample}_/g" | sed 's/_H1//g' | sed 's/_H3//g' | sed 's/_N1//g' | sed 's/_N2//g' | sed s@-@/@g | sed s/_A_/_/g ; fi >> ${type}/${fragment}.txt; done; done; done' >> _03_post_processing.sh
-
-echo 'grep -w 'B__' irma_stats.txt | cut -f1 | while read sample; do cat B_fragment_list.txt | while read fragment; do if test -f ${sample}/${fragment}*.fasta; then cat ${sample}/${fragment}*.fasta | sed "s/^>/\>${sample}_/g" | sed s/_H1//g | sed s/_H3//g | sed s/_N1//g | sed s/_N2//g | sed s@-@/@g | sed s/_B_/_/g ; fi >> B/${fragment}.txt; done; done' >> _03_post_processing.sh
-
-echo 'grep -w 'C__' irma_stats.txt | cut -f1 | while read sample; do cat C_fragment_list.txt | while read fragment; do if test -f ${sample}/${fragment}*.fasta; then cat ${sample}/${fragment}*.fasta | sed "s/^>/\>${sample}_/g" | sed s/_H1//g | sed s/_H3//g | sed s/_N1//g | sed s/_N2//g | sed s@-@/@g | sed s/_C_/_/g ; fi >> C/${fragment}.txt; done; done' >> _03_post_processing.sh
-
-echo 'cat ../samples_id.txt | while read in; do cat ${in}/*.fasta | sed "s/^>/\>${in}_/g" | sed 's/_H1//g' | sed 's/_H3//g' | sed 's/_N1//g' | sed 's/_N2//g' | sed 's@-@/@g' | sed 's/_A_/_/g' | sed 's/_B_/_/g' | sed 's/_C_/_/g' >> all_samples_completo.txt; done' >> _03_post_processing.sh
-
-echo 'sed "s/__//g" irma_stats.txt > clean_irma_stats.txt' >> _03_post_processing.sh
-echo 'sed "s/_\t/\t/g" irma_stats.txt > clean_irma_stats.txt' >> _03_post_processing.sh
+echo 'sed "s/__//g" irma_stats.txt | sed "s/_\t/\t/g" > clean_irma_stats.txt' >> _03_post_processing.sh

bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/postprocessing.sh

@@ -0,0 +1,57 @@
+#CLEAN
+if test -f all_samples_completo.txt; then rm all_samples_completo.txt; fi
+if test -d A_*; then rm -rf A_*; fi
+if test -d B; then rm -rf B; fi
+if test -d C; then rm -rf C; fi
+if test -d D; then rm -rf D; fi
+
+cat ../samples_id.txt | while read sample; do
+    FLUSUBTYPE=$(ls ${sample}/*H*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | cut -d '_' -f1,3 | sort -u)
+    FLUTYPE=$(ls ${sample}/*H*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | cut -d '_' -f1 | sort -u)
+    mkdir -p $FLUSUBTYPE
+    ls ${sample}/amended_consensus/*.fa | cut -d '_' -f3 | cut -d '.' -f1 | while read fragment; do
+        if [ $fragment == 1 ]; then
+            if [ $FLUTYPE == "B" ]; then
+                cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_1/_PB1/' | tee -a ${FLUSUBTYPE}/B_PB1.txt all_samples_completo.txt > /dev/null
+            else
+                cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_1/_PB2/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_PB2.txt all_samples_completo.txt > /dev/null
+            fi
+        elif [ $fragment == 2 ]; then
+            if [ $FLUTYPE == "B" ]; then
+                cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_2/_PB2/' | tee -a ${FLUSUBTYPE}/B_PB2.txt all_samples_completo.txt > /dev/null
+            else
+                cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_2/_PB1/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_PB1.txt all_samples_completo.txt > /dev/null
+            fi
+        elif [ $fragment == 3 ]; then
+            if [ $FLUTYPE == "B" ] || [ $FLUTYPE == "A" ]; then
+                cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_3/_PA/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_PA.txt all_samples_completo.txt > /dev/null
+            else
+                cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_3/_P3/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_P3.txt all_samples_completo.txt > /dev/null
+            fi
+        elif [ $fragment == 4 ]; then
+            if [ $FLUTYPE == "B" ] || [ $FLUTYPE == "A" ]; then
+                cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_4/_HA/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_HA.txt all_samples_completo.txt > /dev/null
+            else
+                cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_4/_HE/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_HE.txt all_samples_completo.txt > /dev/null
+            fi
+        elif [ $fragment == 5 ]; then
+            cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_5/_NP/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_NP.txt all_samples_completo.txt > /dev/null
+        elif [ $fragment == 6 ]; then
+            if [ $FLUTYPE == "B" ] || [ $FLUTYPE == "A" ]; then
+                cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_6/_NA/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_NA.txt all_samples_completo.txt > /dev/null
+            else
+                cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_6/_MP/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_MP.txt all_samples_completo.txt > /dev/null
+            fi
+        elif [ $fragment == 7 ]; then
+            if [ $FLUTYPE == "B" ] || [ $FLUTYPE == "A" ]; then
+                cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_7/_MP/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_MP.txt all_samples_completo.txt > /dev/null
+            else
+                cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_7/_NS/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_NS.txt all_samples_completo.txt > /dev/null
+            fi
+        elif [ $fragment == 8 ]; then
+            cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_8/_NS/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_NS.txt all_samples_completo.txt > /dev/null
+        else
+            echo "The sample $sample has a segment with number $fragment, but I don't know which segment it is."
+        fi
+    done
+done

bu_isciii/templates/IRMA/DOC/irma_config.sh

@@ -5,3 +5,7 @@ MATCH_PROC=8		# grid maximum processes for the MATCH
 SORT_PROC=8		# currently not used
 ALIGN_PROC=8		# grid maximum processes for the rough align
 ASSEM_PROC=8		# grid maximum processes for assembly
+
+### AMENDED CONSENSUS ###
+MIN_AMBIG=0.75          # Sets ambiguities to off
+MIN_CONS_SUPPORT=9      # Mask low coverage <= 9 (10 is ok)

bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog

@@ -53,7 +53,7 @@ cat <<EOF > _01_emmtyper.sbatch
 # create results folder
 mkdir -p 01-typing
 mkdir -p 01-typing/tmps
-blastdb_path=/data/bi/references/cdc_emm_blastdb
+blastdb_path=/data/bi/references/cdc_emm_blastdb/20240509
 
 # Run emmtyper
 singularity exec \\
@@ -63,9 +63,9 @@ singularity exec \\
     /data/bi/pipelines/singularity-images/singularity-emmtyper.0.2.0--py_0 emmtyper \\
     -w blast \\
     --keep \\
-    --blast_db "\${blastdb_path}/cdc_emm_database29042024" \\
-    --percent-identity 95 \\
-    --culling-limit 5 \\
+    --blast_db "\${blastdb_path}/cdc_emm_database" \\
+    --percent-identity 100 \\
+    --culling-limit 5 \
     --output 01-typing/results_emmtyper.out \\
     --output-format verbose \\
     ./fasta_inputs/*.fasta

bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog

@@ -22,7 +22,7 @@ echo "srun --partition short_idx --time 2:00:00 --chdir ${scratch_dir} --output
 
 ## 4-5. Lablog for annotating whole genome samples using Variant Effect Predictor (VEP).
 
-echo "srun --partition short_idx --mem 100G --time 4:00:00 --chdir ${scratch_dir} --output logs/VEP.log --job-name VEP singularity exec -B ${scratch_dir}/../../../ /data/bi/pipelines/singularity-images/ensembl-vep:103.1--pl5262h4a94de4_2 vep --fasta /data/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome/human_g1k_v37.fasta -i ${scratch_dir}/vep/variants_fil_mod.vcf -o ${scratch_dir}/vep/vep_annot.vcf --cache --offline --dir_cache /data/bi/references/eukaria/homo_sapiens/cache_vep/ --everything --dir_plugins /data/bi/references/eukaria/homo_sapiens/cache_vep/Plugins/ --assembly GRCh37 --tab --plugin dbNSFP,/data/bi/references/eukaria/homo_sapiens/cache_vep/custom_databases/dbNSFP/GRCh37/dbNSFP4.1a_grch37.gz,clinvar_id,clinvar_trait,clinvar_OMIM_id,clinvar_Orphanet_id,HGVSc_snpEff,HGVSp_snpEff,SIFT_score,SIFT_pred,Polyphen2_HDIV_score,Polyphen2_HDIV_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,MutationTaster_score,MutationTaster_pred,MutationAssessor_score,MutationAssessor_pred,FATHMM_score,FATHMM_pred,PROVEAN_score,PROVEAN_pred,VEST4_score,MetaSVM_score,MetaSVM_pred,MetaLR_score,MetaLR_pred,CADD_raw,CADD_phred,CADD_raw_hg19,CADD_phred_hg19,GERP++_NR,GERP++_RS,phyloP100way_vertebrate,phastCons100way_vertebrate &" > _02_vep_annotation.sh
+echo "srun --partition short_idx --mem 100G --time 4:00:00 --chdir ${scratch_dir} --output logs/VEP.log --job-name VEP singularity exec -B /data/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome/ -B /data/bi/references/eukaria/homo_sapiens/cache_vep/homo_sapiens -B /data/bi/references/eukaria/homo_sapiens/cache_vep/custom_databases/dbNSFP/GRCh37/ -B ${scratch_dir}/../../../ /data/bi/pipelines/singularity-images/ensembl-vep:103.1--pl5262h4a94de4_2 vep --fasta /data/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome/human_g1k_v37.fasta -i ${scratch_dir}/vep/variants_fil_mod.vcf -o ${scratch_dir}/vep/vep_annot.vcf --cache --offline --dir_cache /data/bi/references/eukaria/homo_sapiens/cache_vep/ --everything --dir_plugins /data/bi/references/eukaria/homo_sapiens/cache_vep/Plugins/ --assembly GRCh37 --tab --plugin dbNSFP,/data/bi/references/eukaria/homo_sapiens/cache_vep/custom_databases/dbNSFP/GRCh37/dbNSFP4.1a_grch37.gz,clinvar_id,clinvar_trait,clinvar_OMIM_id,clinvar_Orphanet_id,HGVSc_snpEff,HGVSp_snpEff,SIFT_score,SIFT_pred,Polyphen2_HDIV_score,Polyphen2_HDIV_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,MutationTaster_score,MutationTaster_pred,MutationAssessor_score,MutationAssessor_pred,FATHMM_score,FATHMM_pred,PROVEAN_score,PROVEAN_pred,VEST4_score,MetaSVM_score,MetaSVM_pred,MetaLR_score,MetaLR_pred,CADD_raw,CADD_phred,CADD_raw_hg19,CADD_phred_hg19,GERP++_NR,GERP++_RS,phyloP100way_vertebrate,phastCons100way_vertebrate &" > _02_vep_annotation.sh
 
 echo "grep -v '^##' ./vep/vep_annot.vcf > ./vep/vep_annot_head.txt" > _03_merge_data1.sh
 echo "sed -i 's/#Uploaded_variation/ID/' ./vep/vep_annot_head.txt" >> _03_merge_data1.sh

bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog

@@ -1,4 +1,4 @@
-# module load Nextflow/22.10.1 singularity
+# module load Nextflow singularity
 
 ln -s ../00-reads/ .
 ln -s ../samples_id.txt .
@@ -28,7 +28,7 @@ cat <<EOF > sarek.sbatch
 
 export NXF_OPTS="-Xms500M -Xmx4G"
 
-nextflow run /data/bi/pipelines/nf-core-sarek/nf-core-sarek-3.4.2/workflow/main.nf \\
+nextflow run /data/bi/pipelines/nf-core-sarek/nf-core-sarek_3.4.4/3_4_4/main.nf \\
 	-c ../../DOC/hpc_slurm_sarek.config \\
 	--input 'samplesheet.csv' \\
 	--outdir 01-sarek \\

bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog

@@ -28,7 +28,7 @@ echo "srun --partition short_idx --time 2:00:00 --chdir ${scratch_dir} --output
 # 3. Lablog for annotating whole genome samples using Variant Effect Predictor (VEP).
 # Run Vep without the plugin columns
 
-echo "srun --partition short_idx --mem 100G --time 12:00:00 --chdir ${scratch_dir} --output logs/VEP.log --job-name VEP singularity exec -B ${scratch_dir}/../../../ /data/bi/pipelines/singularity-images/ensembl-vep:103.1--pl5262h4a94de4_2 vep --fasta /data/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome/human_g1k_v37.fasta -i ${scratch_dir}/vep/variants_fil_mod.vcf -o ${scratch_dir}/vep/vep_annot.vcf --cache --offline --dir_cache /data/bi/references/eukaria/homo_sapiens/cache_vep/ --everything --assembly GRCh37 --tab &" > _02_vep_annotation.sh
+echo "srun --partition short_idx --mem 100G --time 12:00:00 --chdir ${scratch_dir} --output logs/VEP.log --job-name VEP singularity exec -B /data/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome -B /data/bi/references/eukaria/homo_sapiens/cache_vep -B ${scratch_dir}/../../../ /data/bi/pipelines/singularity-images/ensembl-vep:103.1--pl5262h4a94de4_2 vep --fasta /data/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome/human_g1k_v37.fasta -i ${scratch_dir}/vep/variants_fil_mod.vcf -o ${scratch_dir}/vep/vep_annot.vcf --cache --offline --dir_cache /data/bi/references/eukaria/homo_sapiens/cache_vep/ --everything --assembly GRCh37 --tab &" > _02_vep_annotation.sh
 
 #--------------------------------------------------------------------------------------------------------------------
 

bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog

@@ -42,7 +42,7 @@ cat <<EOF > sarek.sbatch
 
 export NXF_OPTS="-Xms500M -Xmx4G"
 
-nextflow run /data/bi/pipelines/nf-core-sarek/nf-core-sarek-3.4.2/workflow/main.nf \\
+nextflow run /data/bi/pipelines/nf-core-sarek/nf-core-sarek_3.4.4/3_4_4/main.nf \\
           -c ../../DOC/hpc_slurm_sarek.config \\
           --input 'samplesheet.csv' \\
           --outdir 01-sarek \\

bu_isciii/templates/mtbseq/ANALYSIS/ANALYSIS01_MTBSEQ/03-MTBSeq/lablog

@@ -13,9 +13,9 @@ cat ../samples_id.txt | xargs -I @@ echo -e "srun --job-name MTBSEQ.@@  --output
 
 # classification
 echo "mkdir classification_all" > _03_gather_results.sh 
-echo "FIRST_SAMPLE=$(head -n1 ../samples_id.txt); head -n 1 ${FIRST_SAMPLE}/Classification/Strain_Classification.tab > classification_all/strain_classification_all.tab; grep \"^'$analysis_year\" */Classification/Strain_Classification.tab | cut -d \":\" -f 2 >> classification_all/strain_classification_all.tab" >> _03_gather_results.sh
+echo 'FIRST_SAMPLE=$(head -n1 samples_id.txt); head -n 1 ${FIRST_SAMPLE}/Classification/Strain_Classification.tab > classification_all/strain_classification_all.tab; grep "^'\'''"$analysis_year"'" */Classification/Strain_Classification.tab | cut -d ":" -f 2 >> classification_all/strain_classification_all.tab' >> _03_gather_results.sh
 # resistances
 echo "mkdir resistances_all" >> _03_gather_results.sh
 cat ../samples_id.txt | xargs -I % echo "cp %/Amend/NONE_joint_cf4_cr4_fr75_ph4_samples1_amended.tab resistances_all/%_var_res.tab" >> _03_gather_results.sh
 # stats
-echo "mkdir stats_all; FIRST_SAMPLE=$(head -n1 ../samples_id.txt); head -n 1 ${FIRST_SAMPLE}/Statistics/Mapping_and_Variant_Statistics.tab > stats_all/statistics_all.tab; grep \"^'$analysis_year\" */Statistics/Mapping_and_Variant_Statistics.tab | cut -d \":\" -f 2 >> stats_all/statistics_all.tab" >> _03_gather_results.sh
+echo 'mkdir stats_all; FIRST_SAMPLE=$(head -n1 ../samples_id.txt); head -n 1 ${FIRST_SAMPLE}/Statistics/Mapping_and_Variant_Statistics.tab > stats_all/statistics_all.tab; grep "^'\'''"$analysis_year"'" */Statistics/Mapping_and_Variant_Statistics.tab | cut -d ":" -f 2 >> stats_all/statistics_all.tab' >> _03_gather_results.sh

bu_isciii/templates/sftp_user.json

@@ -44,7 +44,7 @@
     "sara.perez": ["GeneticDiagnosis"],
     "sbarturen": ["Labvirushep"],
     "sergio.sanchez": ["LabFWDB_ssanchez"],
-    "sherrera": ["LabFWBD", "LabFWBD_ext"],
+    "sherrera": ["LabFWBD", "LabFWBD_ext", "Labtuberculosis"],
     "sresino": ["Labvirushep"],
     "svaldezate": ["Labtaxonomia"],
     "svazquez": ["Labvirusres"],