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Merge pull request #239 from BU-ISCIII/develop
Release 2.1.0 from develop.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -262,13 +262,34 @@ def create_structure(self): | |
| return | ||
|
|
||
| def post_delivery_info(self): | ||
| delivery_notes = bu_isciii.utils.ask_for_some_text( | ||
| msg="Write some delivery notes:" | ||
| ) | ||
| if bu_isciii.utils.prompt_yn_question( | ||
| msg="Do you wish to provide a text file for delivery notes?", dflt=False | ||
| ): | ||
| for i in range(3, -1, -1): | ||
| self.provided_txt = bu_isciii.utils.prompt_path( | ||
| msg="Write the path to the file with RAW text as delivery notes" | ||
| ) | ||
| if not os.path.isfile(os.path.expanduser(self.provided_txt)): | ||
| stderr.print(f"Provided file doesn't exist. Attempts left: {i}") | ||
| else: | ||
| stderr.print(f"File selected: {self.provided_txt}") | ||
| break | ||
| else: | ||
| stderr.print("No more attempts. Delivery notes will be given by prompt") | ||
| self.provided_txt = None | ||
| else: | ||
| self.provided_txt = None | ||
|
|
||
| if self.provided_txt: | ||
| with open(os.path.expanduser(self.provided_txt)) as f: | ||
| self.delivery_notes = " ".join([x.strip() for x in f.readlines()]) | ||
| else: | ||
| self.delivery_notes = bu_isciii.utils.ask_for_some_text( | ||
| msg="Write some delivery notes:" | ||
| ) | ||
| delivery_dict = { | ||
| "resolution_number": self.resolution_id, | ||
| "delivery_notes": delivery_notes, | ||
| "delivery_notes": self.delivery_notes, | ||
| } | ||
|
|
||
| # How json should be fully formatted: | ||
|
|
@@ -568,9 +589,15 @@ def email_creation(self): | |
| if bu_isciii.utils.prompt_yn_question( | ||
| "Do you want to add some delivery notes to the e-mail?", dflt=False | ||
| ): | ||
| email_data["email_notes"] = bu_isciii.utils.ask_for_some_text( | ||
| msg="Write email notes" | ||
| ) | ||
| if self.provided_txt: | ||
| if bu_isciii.utils.prompt_yn_question( | ||
| f"Do you want to use notes from {self.provided_txt}?", dflt=False | ||
| ): | ||
| email_data["email_notes"] = self.delivery_notes | ||
| else: | ||
| email_data["email_notes"] = bu_isciii.utils.ask_for_some_text( | ||
| msg="Write email notes" | ||
| ) | ||
|
|
||
| email_data["user_data"] = self.resolution_info["service_user_id"] | ||
| email_data["service_id"] = self.service_name.split("_", 5)[0] | ||
|
|
@@ -604,7 +631,7 @@ def send_email(self, html_text, results_pdf_file): | |
| server.login(user=email_host_user, password=email_host_password) | ||
| except Exception as e: | ||
| stderr.print("[red] Unable to send e-mail" + e) | ||
|
|
||
| default_cc = "[email protected]" | ||
| msg = MIMEMultipart("alternative") | ||
| msg["To"] = self.resolution_info["service_user_id"]["email"] | ||
| msg["From"] = email_host_user | ||
|
|
@@ -617,18 +644,21 @@ def send_email(self, html_text, results_pdf_file): | |
| + self.service_name.split("_", 5)[2] | ||
| ) | ||
| if bu_isciii.utils.prompt_yn_question( | ||
| "Do you want to add any other sender? appart from " | ||
| + self.resolution_info["service_user_id"]["email"], | ||
| "Do you want to add any other sender? apart from %s. Note: %s is the default CC." | ||
| % (self.resolution_info["service_user_id"]["email"], default_cc), | ||
| dflt=False, | ||
| ): | ||
| stderr.print( | ||
| "[red] Write emails to be added in semicolon separated format: bioinformatica@isciii.es;icuesta@isciii.es" | ||
| "[red] Write emails to be added in semicolon separated format: icuesta@isciii.es;user2@isciii.es" | ||
| ) | ||
| msg["CC"] = bu_isciii.utils.ask_for_some_text(msg="E-mails:") | ||
| rcpt = msg["CC"].split(";") + [msg["To"]] | ||
| cc_address = bu_isciii.utils.ask_for_some_text(msg="E-mails:") | ||
| else: | ||
| rcpt = self.resolution_info["service_user_id"]["email"] | ||
|
|
||
| cc_address = str() | ||
| if cc_address: | ||
| msg["CC"] = str(default_cc + ";" + str(cc_address)) | ||
| else: | ||
| msg["CC"] = default_cc | ||
| rcpt = msg["CC"].split(";") + [msg["To"]] | ||
| html = MIMEText(html_text, "html") | ||
| msg.attach(html) | ||
| with open(results_pdf_file, "rb") as f: | ||
|
|
@@ -639,7 +669,6 @@ def send_email(self, html_text, results_pdf_file): | |
| filename=str(os.path.basename(results_pdf_file)), | ||
| ) | ||
| msg.attach(attach) | ||
|
|
||
| server.sendmail( | ||
| email_host_user, | ||
| rcpt, | ||
|
|
||
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2 changes: 1 addition & 1 deletion
2
...i/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/01-preprocessing/lablog
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9 changes: 6 additions & 3 deletions
9
...sciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/run/lablog
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,13 +1,16 @@ | ||
| # conda activate ariba | ||
| # ARIBA runs local assembli/processing_Data/bioinformatics/services_and_colaborations/CNM/bacteriologia/20190821_QCASSEMBLT_s.gonzalez_T/RAW/fastqc_2/. | ||
|
|
||
| mkdir logs | ||
| scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g') | ||
| downloaded_ref=$(find ../../../../REFERENCES/ -type d -name 'ref_db') | ||
|
|
||
| # Cartesian product of the two files to avoid double looping | ||
| join -j 2 ../../samples_id.txt ../databases.txt | sed 's/^ //g' > sample_database.txt | ||
|
|
||
| # col 1 (arr[0]): sample | ||
| # col 2 (arr[1]): database | ||
| cat sample_database.txt | while read in; do arr=($in); echo "mkdir -p ${arr[0]}; srun --chdir $scratch_dir --output logs/ARIBA${arr[0]}_${arr[1]}.%j.log --job-name ARIBA_${arr[0]}_${arr[1]} --cpus-per-task 5 --mem 5G --partition short_idx --time 02:00:00 ariba run /data/bi/references/ariba/20211216/${arr[1]}/out.${arr[1]}.prepareref ../../../*ASSEMBLY/01-preprocessing/trimmed_sequences/${arr[0]}_1.trim.fastq.gz ../../../*ASSEMBLY/01-preprocessing/trimmed_sequences/${arr[0]}_2.trim.fastq.gz ${arr[0]}/out_${arr[1]}_${arr[0]}_run &"; done > _01_ariba.sh | ||
| cat sample_database.txt | while read in; do arr=($in); echo "mv ${arr[0]}/out_${arr[1]}_${arr[0]}_run/report.tsv ${arr[0]}/out_${arr[1]}_${arr[0]}_run/${arr[0]}_${arr[1]}_report.tsv"; done > _02_fix_tsvreport.sh | ||
| cat sample_database.txt | grep -v 'pubmlst' | while read in; do arr=($in); echo "mkdir -p ${arr[0]}; srun --chdir $scratch_dir --output logs/ARIBA_${arr[0]}_${arr[1]}.%j.log --job-name ARIBA_${arr[0]}_${arr[1]} --cpus-per-task 5 --mem 5G --partition short_idx --time 02:00:00 ariba run /data/bi/references/ariba/20211216/${arr[1]}/out.${arr[1]}.prepareref ../../01-preprocessing/${arr[0]}/${arr[0]}_R1_filtered.fastq.gz ../../01-preprocessing/${arr[0]}/${arr[0]}_R2_filtered.fastq.gz ${arr[0]}/out_${arr[1]}_${arr[0]}_run &"; done > _01_ariba.sh | ||
|
|
||
| cat ../samples_id.txt | while read in; echo "mkdir -p ${arr[0]}; srun --chdir $scratch_dir --output logs/ARIBA_${in}_pubmlst.%j.log --job-name ARIBA_${in}_pubmlst --cpus-per-task 5 --mem 5G --partition short_idx --time 02:00:00 ariba run ${downloaded_ref} ../../01-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../../01-preprocessing/${in}/${in}_R2_filtered.fastq.gz ${in}/out_pubmlst_${in}_run &"; done > _01_ariba.sh | ||
|
|
||
| cat sample_database.txt | while read in; do arr=($in); echo "mv ${arr[0]}/out_${arr[1]}_${arr[0]}_run/report.tsv ${arr[0]}/out_${arr[1]}_${arr[0]}_run/${arr[0]}_${arr[1]}_report.tsv"; done > _02_fix_tsvreport.sh |
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4 changes: 0 additions & 4 deletions
4
bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/lablog
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,2 @@ | ||
| ln -s ../samples_id.txt . | ||
| ln -s ../00-reads . | ||
| mkdir 01-preprocessing | ||
| mkdir 02-srst2 | ||
| mkdir 03-ariba | ||
| mkdir 99-stats |
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